EP3835310A1 - Fibronectinbasierte gerüstdomänenproteine zur bindung an myostatin - Google Patents

Fibronectinbasierte gerüstdomänenproteine zur bindung an myostatin Download PDF

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Publication number
EP3835310A1
EP3835310A1 EP20206702.1A EP20206702A EP3835310A1 EP 3835310 A1 EP3835310 A1 EP 3835310A1 EP 20206702 A EP20206702 A EP 20206702A EP 3835310 A1 EP3835310 A1 EP 3835310A1
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Prior art keywords
seq
myostatin
adnectin
amino acid
group
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Granted
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EP20206702.1A
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English (en)
French (fr)
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EP3835310B1 (de
Inventor
Sharon Cload
Linda Engle
Dasa Lipovsek
Malavi Madireddi
Ginger Chao RAKESTRAW
Joanna F. Swain
Wenjun Zhao
Hui WEI
Aaron P. YAMNIUK
Alexander T. KOZHICH
Vidhyashankar Ramamurthy
Martin J. Corbett
Stanley Richard KRYSTEK, Jr.
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Bristol Myers Squibb Co
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Bristol Myers Squibb Co
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Application filed by Bristol Myers Squibb Co filed Critical Bristol Myers Squibb Co
Priority to SI201332082T priority Critical patent/SI3835310T1/sl
Priority to HRP20240676TT priority patent/HRP20240676T1/hr
Priority to RS20240550A priority patent/RS65556B1/sr
Priority to EP24163980.6A priority patent/EP4397675A3/de
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Definitions

  • the present invention relates to fibronectin-based scaffold domain proteins that bind myostatin.
  • the invention also relates to the use of the innovative proteins in therapeutic applications to treat muscle-wasting diseases and metabolic disorders.
  • the invention further relates to cells comprising such proteins, polynucleotides encoding such proteins or fragments thereof, and to vectors comprising the polynucleotides encoding the innovative proteins.
  • Myostatin also known as growth and differentiation factor-8 (GDF-8), is a member of the transforming growth factor- ⁇ (TGF- ⁇ ) superfamily of secreted growth factors.
  • TGF- ⁇ transforming growth factor- ⁇
  • Myostatin has all of the structural features common to the TGF- ⁇ family proteins: a hydrophobic amino-terminus that acts as a secretory signal, nine invariant cysteine residues, and an "RXXR" furin-type proteolytic processing site. Proteolytic cleavage of the protein gives rise to a C-terminal domain which forms a homodimer that is the biologically active form of myostatin ( Thies et al., Growth Factors 2001;18(4):251-9 ).
  • Myostatin expression is limited primarily to skeletal muscle and adipose tissue, where it has been shown to be a negative regulator of skeletal muscle development ( Lee LS, Immunol Endocr Metab Agents Med Chem. 2010;10:183-194 ).
  • skeletal muscle appears to be the principal target tissue of myostatin, where it binds to cell-surface receptors, leading to muscle loss.
  • Mice and cattle with genetic deficiencies in myostatin exhibit dramatic increases in skeletal muscle mass, i.e., the "double muscling" phenotype, therefore supporting the role of myostatin in suppressing muscle growth ( McPherron and Lee, Proc Natl Acad Sci USA. 2003 Dec 23;100(26):15842-6 ).
  • Muscle hypertrophy in Belgian Blue and Piedmontese cattle breeds is due to a missense mutation within the third exon of the bovine myostatin gene ( Bass et. al., Domest Anim Endocrinol. 1999;17(2-3):191-7 ).
  • Transgenic overexpression of myostatin inhibitors also results in hyper-muscularity.
  • Enhanced muscle growth in these animals is due to an increase in both cell number, or hyperplastic growth, and cell size, or hypertrophic growth, which results in larger and heavier myofibers.
  • Increased skeletal muscle mass due to a myostatin mutation has also been reported in humans. Myostatin inhibition effectively increases skeletal muscle mass and strength, both in the postnatal period and in adults.
  • myostatin regulates energy metabolism and that its inhibition can significantly attenuate the progression of metabolic diseases, including obesity and diabetes.
  • myostatin null mice exhibit decreased body fat accumulation ( McPherron & Lee, J. JCI 109:595, 2002 ) when compared with wild type mice of the same age. This reduction in body fat is a manifestation of reduced adipocyte number and size, implicating a significant role of myostatin in adipogenesis as well as in myogenesis.
  • myostatin is a desirable target for therapeutic or prophylactic intervention for the treatment of disorders or conditions which would benefit from an increase in muscle mass, muscle strength and/or metabolism (e.g., muscular dystrophy, frailty, disuse atrophy and cachexia), disorders associated with muscle wasting (e.g., renal disease, cardiac failure or disease, and liver disease), and metabolic disorders (e.g., Type II diabetes, metabolic syndrome, obesity and osteoarthritis).
  • muscle mass e.g., muscular dystrophy, frailty, disuse atrophy and cachexia
  • disorders associated with muscle wasting e.g., renal disease, cardiac failure or disease, and liver disease
  • metabolic disorders e.g., Type II diabetes, metabolic syndrome, obesity and osteoarthritis.
  • fibronectin domain scaffold proteins that bind myostatin for the therapeutic treatment of, e.g., metabolic disorders, muscle wasting disorders, and muscle loss due to inactivity.
  • the present invention is based, at least in part, on the discovery of Adnectins that bind to and antagonize myostatin.
  • the anti-myostatin Adnectins of the present invention inhibit myostatin activity, thereby affecting downstream SMAD signaling.
  • One mechanism accounting for altered SMAD signaling of some of the anti-myostatin Adnectins of the invention involves the inhibition of Alk4 recruitment to the myostatin-ActRIIb complex, the physiological consequences of which are increased muscle volume and body weight.
  • the invention provides a polypeptide comprising a fibronectin tenth type III domain ( 10 Fn3) wherein the 10 Fn3 has at least one loop selected from loop BC, DE, and FG with an altered amino acid sequence relative to the sequence of the corresponding loop of the human 10 Fn3 domain, and wherein the polypeptide binds myostatin.
  • the polypeptide binds myostatin with a K D of less than 500 nM.
  • the BC loop of the polypeptide of the invention comprises an amino acid sequence according to the formula X 1 -L-P-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 , wherein (a) X 1 is selected from the group consisting of S, T and Y; (b) X 2 is selected from the group consisting of H, Y, N, R, F, G, S and T; (c) X 3 is selected from the group consisting of A, P, Q, S, F, H, N and R; (d) X 4 is selected from the group consisting of G and A; (e) X 5 is selected from the group consisting of H, L, R, V, N, D, F, I and K; (f) X 6 is selected from the group consisting of A, L, G, M, F, I and V; and (g) X 7 is selected from the group consisting of H and N.
  • X 1 is selected from the group consisting of S, T and Y
  • X 1 is S
  • X 2 is H or Y
  • X 3 is A or P
  • X 4 is G
  • X 5 is H
  • L or R is A or L
  • X 6 is A or L
  • X 7 is H.
  • the BC loop comprises an amino acid sequence according to the formula X 19 -X 20 -P-X 21 -G-X 22 -A, wherein (a) X 19 is selected from the group consisting of D, E, V and W; (b) X 20 is selected from the group consisting of A, S and V; (c) X 21 is selected from the group consisting of R, A, G, K and L; and (d) X 22 is selected from the group consisting of L and R.
  • X 19 is D
  • X 20 is A, S or V
  • X 22 is L.
  • the DE loop comprises an amino acid sequence according to the formula G-R-G-X 8 , wherein X 8 is V or L.
  • the DE loop comprises an amino acid sequence according to the formula X 23 -G-R-G-X 24 , wherein (a) X 23 is selected from the group consisting of V, P, F, I and L; and (b) X 24 is selected from the group consisting of S, N and T.
  • the FG loop of the polypeptide of the invention comprises an amino acid sequence according to the formula X 9 -X 10 -X 11 -X 12 -X 13 -X 14 -X 15 -X 16 -X 17 -X 18 , wherein (a) X 9 is selected from the group consisting of L, V and I; (b) X 10 is selected from the group consisting of T and S; (c) X 11 is selected from the group consisting of K, R, A, G, S, D, H, N, T and P; (d) X 12 is selected from the group consisting of S, T, A, E, H, K and N; (e) X 13 is selected from the group consisting of K, G, Q, D, E, N, T and S; (f) X 14 is selected from the group consisting of V, I, F, L, M, P, T and Y; (g) X 15 is selected from the group consisting of I, L and Y; (h)
  • X 9 is L or V
  • X 10 is T
  • X 11 is K or R
  • X 12 is S or T
  • X 13 is K
  • X 14 is V or I
  • X 15 is I
  • X 16 is H
  • X 17 is Y and/or X 18 is K or M.
  • the FG loop comprises an amino acid sequence according to the formula X 25 -X 26 -R-X 27 -G-X 28 -X 29 -X 30 -X 31 -X 32 , wherein (a) X 25 is selected from the group consisting of I and V; (b) X 26 is selected from the group consisting of F, D and Y; (c) X 27 is selected from the group consisting of D and T; (d) X 28 is selected from the group consisting of P, M, V and T; (e) X 29 is selected from the group consisting of V, L, N, R and S; (f) X 30 is selected from the group consisting of H, T, L, N, Q and S; (g) X 31 is selected from the group consisting of F, W, Y, H and L; and (h) X 32 is selected from the group consisting of D, A and G.
  • X 25 is I
  • X 26 is F
  • X 27 is D
  • X 28 is P
  • X 29 is V
  • X 30 is H or T
  • X 31 is F or W
  • X 32 is D.
  • the polypeptide comprises a BC loop and a DE loop, or a BC loop and FG loop, or a DE loop and an FG loop, or a BC loop, a DE loop and an FG loop.
  • the BC loop of the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 7-38.
  • the DE loop comprises an amino acid selected from the group consisting of SEQ ID NOs: 39-45.
  • the FG loop comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 46-79.
  • the BC, DE, or FG loop amino acid sequence is at least 80% identical to any one of SEQ ID NOs: 7-38, 39-45, and 46-79, respectively.
  • the polypeptide comprises an amino acid sequence that is at least 80%, 85%, 90%, 95%, 98%, or 99% identical to any one of SEQ ID NOs: 80-123, 228-239, and 252-273. In yet other embodiments, the polypeptide comprises an amino acid sequence selected from the group consisting of SEQ ID NOs: 80-123, 228-239, and 252-273.
  • the polypeptides comprise the BC, DE, and FG loop combinations as shown in Table 1.
  • the polypeptide has the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively.
  • the polypeptide comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the BC loop has 1, 2, 3, 4, 5, or 6 amino acid substitutions, such as conservative amino acid substitutions.
  • the BC loop has an amino acid sequence according to the formula X 33 -L-P-X 34 -X 35 -X 36 -X 37 -X 38 -X 39 , wherein X 33 is T or Y; X 34 is Y, N, R, F, G, S, or T; X 35 is A, P, S, F, H, N, or R; X 36 is A; X 37 is H, L, R, V, N, D, F, or I; X 38 is L, G, M, F, I, or V; and X 39 is H.
  • the polypeptide comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the DE loop has 1 amino acid substitution, such as a conservative amino acid substitution.
  • the DE loop has an amino acid sequence according to the formula G-R-G-X 40 , wherein X 40 is L.
  • the polypeptide comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the FG loop has 1, 2, 3, 4, 5, 6, 7, or 8 amino acid substitutions, such as conservative amino acid substitutions.
  • the FG loop has an amino acid sequence according to the formula X 41 -X 42 -X 43 -X 44 -X 45 -X 46 -X 47 -X 48 -X 49 -X 50 , wherein X 41 is L or I; X 42 is S; X 43 is K, R, A, G, S, H, N, T, or P; X 44 is S, A, E, H, K, or N; X 45 is K, Q, D, E, N, T, or S; X 46 is V, I, F, L, M, P, or T; X 47 is I or Y; X 48 is H, I, V, L, R, F, G, S, or T; X 49 is H; and X 50 is M, L, R, or V.
  • the polypeptide comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the BC loop has 1, 2, 3, 4, 5, or 6 amino acid substitutions, such as conservative amino acid substitutions, and the DE loop has 1 amino acid substitution, such as a conservative amino acid substitution.
  • the BC loop has an amino acid sequence according to the formula X 33 -L-P-X 34 -X 35 -X 36 -X 37 -X 38 -X 39 , wherein X 33 is T or Y; X 34 is Y, N, R, F, G, S, or T; X 35 is A, P, S, F, H, N, or R; X 36 is A; X 37 is H, L, R, V, N, D, F, or I; X 38 is L, G, M, F, I, or V; and X 39 is H, and the DE loop has an amino acid sequence according to the formula G-R-G-X 40 , wherein X 40 is L.
  • the polypeptide comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the BC loop has 1, 2, 3, 4, 5, or 6 amino acid substitutions, such as conservative amino acid substitutions, and the FG loop has 1, 2, 3, 4, 5, 6, 7, or 8 amino acid substitutions, such as conservative amino acid substitutions.
  • the BC loop has an amino acid sequence according to the formula X 33 -L-P-X 34 -X 35 -X 36 -X 37 -X 38 -X 39 , wherein X 33 is T or Y; X 34 is Y, N, R, F, G, S, or T; X 35 is A, P, S, F, H, N, or R; X 36 is A; X 37 is H, L, R, V, N, D, F, or I; X 38 is L, G, M, F, I, or V; and X 39 is H, and the FG loop has an amino acid sequence according to the formula X 41 -X 42 -X 43 -X 44 -X 45 -X 46 -X 47 -X 48 -X 49 -X 50 , wherein X 41 is L or I; X 42 is S; X 43 is K, R, A, G, S, H, N, T, or P; X 44 is S, A, E,
  • the polypeptide comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein and the DE loop has 1 amino acid substitution, such as a conservative amino acid substitution, and the FG loop has 1, 2, 3, 4, 5, 6, 7, or 8 amino acid substitutions, such as conservative amino acid substitutions.
  • the DE loop has an amino acid sequence according to the formula G-R-G-X 40 , wherein X 40 is L, and the FG loop has an amino acid sequence according to the formula X 41 -X 42 -X 43 -X 44 -X 45 -X 46 -X 47 -X 48 -X 49 -X 50 , wherein X 41 is L or I; X 42 is S; X 43 is K, R, A, G, S, H, N, T, or P; X 44 is S, A, E, H, K, or N; X 45 is K, Q, D, E, N, T, or S; X 46 is V, I, F, L, M, P, or T; X 47 is I or Y; X 48 is H, I, V, L, R, F, G, S, or T; X 49 is H; and X 50 is M, L, R, or V.
  • the polypeptide comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the BC loop has 1, 2, 3, 4, 5, or 6 amino acid substitutions, such as conservative amino acid substitutions, and the DE loop has 1 amino acid substitution, such as a conservative amino acid substitution, and the FG loop has 1, 2, 3, 4, 5, 6, 7, or 8 amino acid substitutions, such as conservative amino acid substitutions.
  • the BC loop has an amino acid sequence according to the formula X 33 -L-P-X 34 -X 35 -X 36 -X 37 -X 38 -X 39 , wherein X 33 is T or Y; X 34 is Y, N, R, F, G, S, or T; X 35 is A, P, S, F, H, N, or R; X 36 is A; X 37 is H, L, R, V, N, D, F, or I; X 38 is L, G, M, F, I, or V; and X 39 is H; the DE loop has an amino acid sequence according to the formula G-R-G-X 40 , wherein X 40 is L; and the FG loop has an amino acid sequence according to the formula X 41 -X 42 -X 43 -X 44 -X 45 -X 46 -X 47 -X 48 -X 49 -X 50 , wherein X 41 is L or I; X 42 is S; X 43
  • the polypeptide comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, and has amino acid substitutions in the BC, DE, and FG loops which allow the polypeptide to maintain binding to myostatin.
  • amino acid substitutions can be determined by, e.g., deep mutational scanning as described in Example 8.
  • the polypeptide has a BC loop comprising an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein: X 51 is selected from the group consisting of A, C, D, F, H, I, K, L, N, Q, R, S, T, V, W, and Y; X 52 is selected from the group consisting of L, M, and V; X 53 is selected from the group consisting of A, C, D, E, I, K, L, M, N, P, Q, R, S, T, V, and Y; X 54 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y; X 55 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M,
  • X 51 is selected from the group consisting of C, F, I, S, V, W, and Y;
  • X 52 is selected from the group consisting of L;
  • X 53 is selected from the group consisting of P;
  • X 54 is selected from the group consisting of C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y;
  • X 55 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;
  • X 56 is selected from the group consisting of G;
  • X 57 is selected from the group consisting of A, C, G, H, I, K, L, M, N, Q, R, S, V, W, and Y;
  • X 58 is selected from the group consisting of A, G, L, M, and S;
  • X 51 is selected from the group consisting of F, S, and W;
  • X 52 is selected from the group consisting of L;
  • X 53 is selected from the group consisting of P;
  • X 54 is selected from the group consisting of C, F, G, I, K, L, M, N, R, S, T, V, W, and Y;
  • X 55 is selected from the group consisting of A, C, E, F, H, I, K, L, M, P, Q, R, S, T, V, and Y;
  • X 56 is selected from the group consisting of G;
  • X 57 is selected from the group consisting of A, C, H, K, L, M, N, R, V, W, and Y;
  • X 58 is selected from the group consisting of A, G, and L;
  • X 59 is selected from the group consisting of H, N, and Q.
  • X 51 S; X 52 is L;
  • X 53 is P;
  • the polypeptide comprises a DE loop comprising an amino acid sequence according to the formula G-R-G-X 60 , wherein X 60 is A, C, D, E, F, I, K, L, M, N, Q, S, T, and V.
  • X 60 is C, E, I, L, M, Q, T, and V.
  • X 60 is C, E, I, L, M, and V.
  • X 60 is V.
  • the polypeptide comprises an FG loop comprising an amino acid sequence according to the formula X 61 -X 62 -X 63 -X 64 -X 65 -X 66 -X 67 -X 68 -X 69 -X 70 , wherein X 61 is selected from the group consisting of A, C, F, I, L, M, Q, T, V, W, and Y; X 62 is selected from the group consisting of A, C, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y; X 63 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; X 64 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V,
  • X 61 is selected from the group consisting of A, C, I, L, M, and V;
  • X 62 is selected from the group consisting of C, F, H, I, L, M, Q, R, S, T, V, W, and Y;
  • X 63 is selected from the group consisting of A, C, D, E, F, G, H, I, L, M, N, P, Q, S, T, V, W, and Y;
  • X 64 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y;
  • X 65 is selected from the group consisting of A, D, E, F, G, H, I, L, M, N, Q, S, T, V, W, and Y;
  • X 66 is selected from the group consisting of C, F, I, L, M, P, T, V, W, and Y
  • X 61 is selected from the group consisting of I and V;
  • X 62 is selected from the group consisting of C, F, I, L, M, T, V, W, and Y;
  • X 63 is selected from the group consisting of A, C, D, E, F, G, H, I, L, M, N, Q, S, T, and V;
  • X 64 is selected from the group consisting of A, C, D, F, G, I, L, M, N, Q, S, T, V, W, and Y;
  • X 65 is selected from the group consisting of A, G, S, T, and W;
  • X 66 is selected from the group consisting of F, I, V, W, and Y;
  • X 67 is selected from the group consisting of F, H, I, L, M, V, W, and Y;
  • X 68 is selected from the group consisting of A, C, F, G, I, K, L, M, T,
  • the polypeptide of the invention comprises BC, DE, and FG loops, wherein the BC loop comprises an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein, X 51 is selected from the group consisting of A, C, D, F, H, I, K, L, N, Q, R, S, T, V, W, and Y; X 52 is selected from the group consisting of L, M, and V; X 53 is selected from the group consisting of A, C, D, E, I, K, L, M, N, P, Q, R, S, T, V, and Y; X 54 is A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y; X 55 is selected from the group consisting of A, C, D, E, F, G,
  • the polypeptide of the invention comprises BC, DE, and FG loops, wherein the BC loop comprises an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein, X 51 is selected from the group consisting of C, F, I, S, V, W, and Y; X 52 is L; X 53 is P; X 54 is selected from the group consisting of C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y; X 55 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; X 56 is G; X 57 is selected from the group consisting of A, C, G, H, I, K, L, M, M; X
  • the polypeptide of the invention comprises BC, DE, and FG loops, wherein the BC loop comprises an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein, X 51 is selected from the group consisting of F, S, and W; X 52 is L; X 53 is P; X 54 is selected from the group consisting of C, F, G, I, K, L, M, N, R, S, T, V, W, and Y; X 55 is selected from the group consisting of A, C, E, F, H, I, K, L, M, P, Q, R, S, T, V, and Y; X 56 is G; X 57 is selected from the group consisting of A, C, H, K, L, M, N, R, V, W, and Y; X 58 is selected from the group consisting of A, G
  • the polypeptide of the invention comprises BC, DE, and FG loops, wherein the BC loop comprises an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein, X 51 is S; X 52 is L; X 53 is P; X 54 is H; X 55 is Q; X 56 is G; X 57 is K; X 58 is A; X 59 is N; the DE loop comprises an amino acid sequence according to the formula G-R-G-X 60 , wherein X 60 is V; and the FG loop comprises an amino acid sequence according to the formula X 61 -X 62 -X 63 -X 64 -X 65 -X 66 -X 67 -X 68 -X 69 -X 70 , wherein X 61 is V; X 62 is T; X 63 is D; X
  • the polypeptide comprises an amino acid sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence set forth in SEQ ID NO: 273 [PRD-1474], SEQ ID NO: 118 [3116_A06], SEQ ID NO: 281 [core Adnectin sequence of PRD-1474 and 3116_A06 preceded by N-terminal extension sequence (GVSDVPRDL) and followed by a C-terminal tail (EI)] or SEQ ID NO: 331 [core Adnectin sequence of PRD-1474 and 3116_A06 without an N-terminal leader sequence or C-terminal tail].
  • the polypeptide comprises an amino acid sequence at least 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to the non-BC, DE, and FG loop regions of SEQ ID NO: 118, 273, 281, or 331.
  • the invention provides for polypeptides which bind to a discontinuous Adnectin binding site on myostatin.
  • the polypeptides bind a region within amino acids 55-66 of myostatin (SEQ ID NO: 3).
  • the polypeptides bind a region within amino acids 85-101 of myostatin (SEQ ID NO: 3).
  • the polypeptides binds within two regions, amino acids 85-101 and 55-66, of myostatin (SEQ ID NO: 3).
  • polypeptides of the invention do not compete for binding to myostatin with ActRIIB. In some embodiments, the polypeptides of the invention compete for binding to myostatin with ALK4 and/or ALK5.
  • the polypeptides described above may comprise one or more pharmacokinetic (PK) moieties such as polyethylene glycol, sialic acid, Fc, Fc fragment, transferrin, serum albumin, a serum albumin binding protein, and a serum immunoglobulin binding protein.
  • PK pharmacokinetic
  • the PK moiety is a serum albumin binding protein that comprises an 10 Fn3 domain which binds to, for example, HSA.
  • the PK moiety is Fc and can be on either the N- or C-terminus of the polypeptide, and optionally form a dimer.
  • the PK moiety is polyethylene glycol.
  • the PK moiety and polypeptide are linked via at least one disulfide bond, a peptide bond, a polypeptide, a polymeric sugar or a polyethylene glycol moiety.
  • the invention provides a pharmaceutical composition comprising a polypeptide described above, which is optionally endotoxin-free.
  • the invention provides an isolated nucleic acid molecule encoding a polypeptide described above, an expression vector comprising a nucleotide sequence, and a cell comprising the nucleic acid encoding the polypeptide.
  • the invention provides a method of producing the anti-myostatin polypeptide by culturing the cell.
  • the invention provides a method of attenuating or inhibiting a myostatin-related disease or disorder in a subject by administering an effective amount of the polypeptide or composition comprising a polypeptide described above.
  • the disease to be treated is muscular dystrophy, amyotrophic lateral sclerosis, inclusion body myositis (IBM), congestive obstructive pulmonary disease, chronic heart failure, cancer, AIDs, renal failure, chronic kidney disease, uremia, rheumatoid arthritis, sarcopenia, muscle wasting due to prolonged bedrest, spinal cord injury, stroke, bone fracture, aging, diabetes, obesity, hyperglycemia, cachexia, osteoarthritis, osteoporosis, myocardial infarction, or fibrosis.
  • IBM inclusion body myositis
  • the invention provides a method of attenuating or inhibiting a disorder associated with degeneration or wasting of muscle in a subject.
  • the invention provides a method of administering the polypeptide to increase muscle mass, increase the number of muscle cells, increase the size of muscle cells, increase muscle strength, physical performance and/or endurance in the subject.
  • the invention provides a method of attenuating or inhibiting a metabolic disorder in a subject.
  • the metabolic disorder is diabetes (e.g., type II diabetes), hyperglycemia, hyperinsulinaemia, hyperlipidaemia, insulin resistance, impaired glucose metabolism, lipodystrophy, obesity, or metabolic syndrome.
  • a second therapeutic composition can be administered.
  • administration of the polypeptide results in increased insulin sensitivity, increased glucose uptake by cells, decreased blood glucose levels, and/or decreased body fat.
  • the invention provides a method for enhancing lean muscle mass in a subject comprising administering an effective amount of a polypeptide or composition described above.
  • the invention provides a method for increasing the ratio of lean muscle mass to fat in a subject comprising administering an effective amount of a polypeptide or composition described above.
  • kits comprising a polypeptide or composition described above, and instructions for use.
  • the invention provides methods of detecting or measuring myostatin in a sample comprising contacting the sample with a polypeptide described above, and detecting or measuring binding of the polypeptide to myostatin.
  • the invention relates to anti-myostatin binding Adnectins for use in attenuating or inhibiting a myostatin-related disease or disorder, attenuating or inhibiting a disorder associated with degeneration or wasting of muscle, increasing muscle mass, increasing the number of muscle cells, increasing the size of muscle cells, increasing muscle strength, physical performance and/or endurance, attenuating or inhibiting a metabolic disorder, enhancing lean muscle mass, and/or increasing the ratio of lean muscle mass to fat, in a subject.
  • the anti-myostatin Adnectins are those described herein, e.g., the anti-myostatin Adnectins set forth in SEQ ID NOs: 80-123, 228-239, and 252-273.
  • the invention relates to the use of the anti-myostatin binding Adnectins for preparing a medicament for attenuating or inhibiting a myostatin-related disease or disorder, attenuating or inhibiting a disorder associated with degeneration or wasting of muscle, increasing muscle mass, increasing the number of muscle cells, increasing the size of muscle cells, increasing muscle strength, physical performance and/or endurance, attenuating or inhibiting a metabolic disorder, enhancing lean muscle mass, and/or increasing the ratio of lean muscle mass to fat, in a subject.
  • the anti-myostatin Adnectins are those described herein, e.g., the anti-myostatin Adnectins set forth in SEQ ID NOs: 80-123, 228-239, and 252-273.
  • “Full-length myostatin” as used herein refers to the full length polypeptide sequence described in McPherron et al. (1997), supra, as well as related full-length polypeptides including allelic variants and interspecies homologs.
  • the term “myostatin” or “mature myostatin” refers to fragments of the biologically active mature myostatin, as well as related polypeptides including allelic variants, splice variants, and fusion peptides and polypeptides.
  • the mature C-terminal protein has been reported to have 100% sequence identity among many species including human, mouse, chicken, porcine, turkey, and rat ( Lee et al., PNAS 2001;98:9306 ).
  • the sequence for human prepromyostatin is:
  • the sequence for mature myostatin (conserved in human, murine, rat, chicken, turkey, dog, horse, and pig) is:
  • Polypeptide refers to any sequence of two or more amino acids, regardless of length, post-translation modification, or function. "Polypeptide,” “peptide,” and “protein” are used interchangeably herein. Polypeptides can include natural amino acids and non-natural amino acids such as those described in U.S. Pat. No. 6,559,126 , incorporated herein by reference.
  • Polypeptides can also be modified in any of a variety of standard chemical ways (e.g., an amino acid can be modified with a protecting group; the carboxy-terminal amino acid can be made into a terminal amide group; the amino-terminal residue can be modified with groups to, e.g., enhance lipophilicity; or the polypeptide can be chemically glycosylated or otherwise modified to increase stability or in vivo half-life).
  • Polypeptide modifications can include the attachment of another structure such as a cyclic compound or other molecule to the polypeptide and can also include polypeptides that contain one or more amino acids in an altered configuration (i.e., R or S; or, L or D).
  • the peptides of the invention are proteins derived from the tenth type III domain of fibronectin that have been modified to bind to myostatin and are referred to herein as, "anti-myostatin Adnectin” or “myostatin Adnectin.”
  • polypeptide chain refers to a polypeptide wherein each of the domains thereof is joined to other domain(s) by peptide bond(s), as opposed to non-covalent interactions or disulfide bonds.
  • an "isolated" polypeptide is one that has been identified and separated and/or recovered from a component of its natural environment. Contaminant components of its natural environment are materials that would interfere with diagnostic or therapeutic uses for the polypeptide, and may include enzymes, hormones, and other proteinaceous or nonproteinaceous solutes.
  • the polypeptide will be purified (1) to greater than 95% by weight of polypeptide as determined by the Lowry method, and most preferably more than 99% by weight, (2) to a degree sufficient to obtain at least residues of N-terminal or internal amino acid sequence by use of a spinning cup sequenator, or (3) to homogeneity by SDS-PAGE under reducing or nonreducing condition using Coomassie blue or, preferably, silver stain.
  • Isolated polypeptide includes the polypeptide in situ within recombinant cells since at least one component of the polypeptide's natural environment will not be present. Ordinarily, however, isolated polypeptide will be prepared by at least one purification step.
  • Percent (%) amino acid sequence identity herein is defined as the percentage of amino acid residues in a candidate sequence that are identical with the amino acid residues in a selected sequence, after aligning the sequences and introducing gaps, if necessary, to achieve the maximum percent sequence identity, and not considering any conservative substitutions as part of the sequence identity. Alignment for purposes of determining percent amino acid sequence identity can be achieved in various ways that are within the skill in the art, for instance, using publicly available computer software such as BLAST, BLAST-2, ALIGN, ALIGN-2 or Megalign (DNASTARTM) software. Those skilled in the art can readily determine appropriate parameters for measuring alignment, including any algorithms needed to achieve maximal alignment over the full-length of the sequences being compared.
  • the % amino acid sequence identity of a given amino acid sequence A to, with, or against a given amino acid sequence B is calculated as follows: 100 times the fraction X/Y where X is the number of amino acid residues scored as identical matches by the sequence alignment program ALIGN-2 in that program's alignment of A and B, and where Y is the total number of amino acid residues in B. It will be appreciated that where the length of amino acid sequence A is not equal to the length of amino acid sequence B, the % amino acid sequence identity of A to B will not equal the % amino acid sequence identity of B to A.
  • “conservative substitution” denotes the replacement of an amino acid residue by another, without altering the overall conformation and function of the peptide, including, but not limited to, replacement of an amino acid with one having similar properties (such as, for example, polarity, hydrogen bonding potential, acidic, basic, shape, hydrophobic, aromatic, and the like).
  • Amino acids with similar properties are well known in the art. For example, arginine, histidine and lysine are hydrophilic-basic amino acids and may be interchangeable. Similarly, isoleucine, a hydrophobic amino acid, may be replaced with leucine, methionine or valine.
  • Neutral hydrophilic amino acids which can be substituted for one another, include asparagine, glutamine, serine and threonine.
  • substituted include asparagine, glutamine, serine and threonine.
  • substituted includes those amino acids that have been altered or modified from naturally occurring amino acids. As such it should be understood that in the context of the present invention a conservative substitution is recognized in the art as a substitution of one amino acid for another amino acid that has similar properties.
  • Adnectin binding site refers to the site or portion of a protein (e.g., myostatin) that interacts or binds to a particular Adnectin (e.g., as an epitope is recognized by an antibody).
  • Adnectin binding sites can be formed from contiguous amino acids or noncontiguous amino acids juxtaposed by tertiary folding of a protein. Adnectin binding sites formed by contiguous amino acids are typically retained on exposure to denaturing solvents, whereas Adnectin binding sites formed by tertiary folding are typically lost on treatment of denaturing solvents.
  • An Adnectin binding site for an anti-myostatin Adnectin of the invention may be determined by application of standard techniques typically used for epitope mapping of antibodies including, but not limited to protease mapping and mutational analysis.
  • an Adnectin binding site can be determined by competition assay using a reference Adnectin or antibody which binds to the same polypeptide, e.g., myostatin (as further described infra in the section "Cross-Competing Adnectins and/or Adnectins that Bind to the Same Adnectin Binding Site.” If the test Adnectin and reference molecule (e.g., another Adnectin or antibody) compete, then they bind to the same Adnectin binding site or to Adnectin binding sites sufficiently proximal such that binding of one molecule interferes with the other.
  • the terms “specifically binds,” “specific binding,” “selective binding,” and “selectively binds,” as used interchangeably herein refers to an Adnectin that exhibits affinity for a myostatin, but does not significantly bind (e.g., less than about 10% binding) to a different polypeptide as measured by a technique available in the art such as, but not limited to, Scatchard analysis and/or competitive binding assays (e.g., competition ELISA, BIACORE assay).
  • the term is also applicable where e.g., a binding domain of an Adnectin of the invention is specific for myostatin.
  • binding refers to the situation in which an Adnectin of the invention binds myostatin at least about 20% greater than it binds a different polypeptide as measured by a technique available in the art such as, but not limited to, Scatchard analysis and/or competitive binding assays (e.g., competition ELISA, BIACORE assay).
  • cross-reactivity refers to an Adnectin which binds to more than one distinct protein having identical or very similar Adnectin binding sites.
  • K D is intended to refer to the dissociation equilibrium constant of a particular Adnectin-protein (e.g., myostatin) interaction or the affinity of an Adnectin for a protein (e.g., myostatin), as measured using a surface plasmon resonance assay or a cell binding assay.
  • a “desired K D ,” as used herein, refers to a K D of an Adnectin that is sufficient for the purposes contemplated.
  • a desired K D may refer to the K D of an Adnectin required to elicit a functional effect in an in vitro assay, e.g., a cell-based luciferase assay.
  • k ass is intended to refer to the association rate constant for the association of an Adnectin into the Adnectin/protein complex.
  • k diss is intended to refer to the dissociation rate constant for the dissociation of an Adnectin from the Adnectin/protein complex.
  • IC 50 refers to the concentration of an Adnectin that inhibits a response, either in an in vitro or an in vivo assay, to a level that is 50% of the maximal inhibitory response, i.e., halfway between the maximal inhibitory response and the untreated response.
  • myostatin activity refers to one or more of growth-regulatory or morphogenetic activities associated with the binding of active myostatin protein to ActRIIb and the subsequent recruitment of Alk4 or Alk5.
  • active myostatin is a negative regulator of skeletal muscle mass.
  • Active myostatin can also modulate the production of muscle-specific enzymes (e.g., creatine kinase), stimulate myoblast proliferation, and modulate preadipocyte differentiation to adipocytes.
  • Myostatin activity can be determined using art-recognized methods, such as those described herein.
  • inhibitor myostatin activity or “antagonize myostatin activity” or “antagonize myostatin” are used interchangeably to refer to the ability of the anti-myostatin Adnectins of the present invention to neutralize or antagonize an activity of myostatin in vivo or in vitro.
  • the terms “inhibit” or “neutralize” as used herein with respect to an activity of an Adnectin of the invention means the ability to substantially antagonize, prohibit, prevent, restrain, slow, disrupt, eliminate, stop, reduce or reverse e.g., progression or severity of that which is being inhibited including, but not limited to, a biological activity or property, a disease or a condition.
  • the inhibition or neutralization is preferably at least about 10%, 20%, 30%, 40%, 50%, 60%, 70%, 80%, 90%, 95% or higher.
  • an anti-myostatin Adnectin of the invention may reduce circulating levels of biologically active myostatin normally found in a vertebrate subject, or a reduction of circulating levels of biologically active myostatin in subjects with disorders that result in elevated circulating levels of myostatin.
  • a reduction of myostatin activity may be determined using in vitro assays, e.g., binding assays, as described herein.
  • a reduction in myostatin activity may result in an increase in body weight, enhanced muscle mass, increased muscle strength, an alteration in the ratio of muscle to fat, an increase in fat-free muscle mass, an increase in the size and/or number of muscle cells, and/or a reduction in body fat content.
  • PK is an acronym for "pharmacokinetic” and encompasses properties of a compound including, by way of example, absorption, distribution, metabolism, and elimination by a subject.
  • a "PK modulation protein” or “PK moiety” as used herein refers to any protein, peptide, or moiety that affects the pharmacokinetic properties of a biologically active molecule when fused to or administered together with the biologically active molecule.
  • Examples of a PK modulation protein or PK moiety include PEG, human serum albumin (HSA) binders (as disclosed in U.S. Publication Nos. 2005/0287153 and 2007/0003549 , PCT Publication Nos. WO 2009/083804 and WO 2009/133208 ), human serum albumin, Fc or Fc fragments and variants thereof, and sugars (e.g., sialic acid).
  • the "half-life" of an amino acid sequence or compound can generally be defined as the time taken for the serum concentration of the polypeptide to be reduced by 50%, in vivo, for example due to degradation of the sequence or compound and/or clearance or sequestration of the sequence or compound by natural mechanisms.
  • the half-life can be determined in any manner known per se, such as by pharmacokinetic analysis.
  • Suitable techniques will be clear to the person skilled in the art, and may for example generally involve the steps of suitably administering to a subject a suitable dose of the amino acid sequence or compound of the invention; collecting blood samples or other samples from the subject at regular intervals; determining the level or concentration of the amino acid sequence or compound of the invention in said blood sample; and calculating, from (a plot of) the data thus obtained, the time until the level or concentration of the amino acid sequence or compound of the invention has been reduced by 50% compared to the initial level upon dosing.
  • Half-life can be expressed using parameters such as the t 1/2 -alpha, t 1/2 -beta, HL_Lambda_z, and the area under the curve (AUC).
  • an “increase in half-life” refers to an increase in any one of these parameters, any two of these parameters, any three of these parameters or all four of these parameters.
  • An “increase in half-life” in particular refers to an increase in the t 1/2 -beta, and/or HL_Lambda_z, either with or without an increase in the t 1/2 -alpha and/or the AUC or both.
  • the terms "individual,” “subject,” and “patient,” used interchangeably herein, refer to an animal, preferably a mammalian (including a nonprimate and a primate) or avian species, including, but not limited to, murines, simians, humans, mammalian farm animals (e.g., bovine, porcine, ovine), mammalian sport animals (e.g., equine), and mammalian pets (e.g., canine and feline); preferably the term refers to humans.
  • mammalian farm animals e.g., bovine, porcine, ovine
  • mammalian sport animals e.g., equine
  • mammalian pets e.g., canine and feline
  • avian species including, but not limited to, chickens and turkeys.
  • the subject preferably a mammal, preferably a human
  • the subject preferably a mammal, preferably a human
  • a therapeutically effective amount refers to at least the minimal dose, but less than a toxic dose, of an agent which is necessary to impart a therapeutic benefit to a subject.
  • a therapeutically effective amount of an anti-myostatin Adnectin of the invention is an amount which in mammals, preferably humans, results in one or more of the following: an increase in muscle volume and/or muscle strength, a decrease in body fat, an increase in insulin sensitivity, or the treatment of conditions wherein the presence of myostatin causes or contributes to an undesirable pathological effect or a decrease in myostatin levels results in a beneficial therapeutic effect.
  • frail or “frailty” as used herein refers to a condition that can be characterized by two or more symptoms from weakness, weight loss, slowed mobility, fatigue, low activity levels, poor endurance, and impaired behavioral response to sensory cues.
  • One hallmark of frailty is "sarcopenia,” or the age-related loss of muscle mass.
  • cachexia refers to the condition of accelerated muscle wasting and loss of lean body mass that can result from various diseases.
  • the present invention provides novel polypeptides that bind to and antagonize myostatin (herein referred to as "anti-myostatin Adnectins").
  • myostatin was presented to large synthetic libraries of Adnectins.
  • Adnectins that bound to myostatin were screened for myostatin binding, for biophysical properties, and for myostatin inhibitory activity.
  • the anti-myostatin Adnectins were mutated and subjected to further selective pressure by lowering the target concentration and selecting for anti-myostatin Adnectins with slow off-rates. From this optimization process, a family of Adnectins was identified as myostatin specific inhibitors with favorable biochemical and biophysical activity.
  • the anti-myostatin Adnectins disclosed in the present application are useful for the treatment of disorders, diseases, and conditions for which inhibition of myostatin activity is known to be beneficial, including, but not limited to, the treatment of muscle wasting diseases, metabolic disorders, and muscle atrophy due to inactivity.
  • the myostatin signaling pathway involves binding of myostatin to ActRIIb, followed by recruitment of activin receptor-like kinase 4 (ALK4) or ALK5. Binding to the ALKs induces Smad2/Smad3 phosphorylation, followed by activation of the TGF ⁇ -like signaling pathway (see, e.g., Rebbapragada et al., MCB 2003;23:7230-42 ).
  • the Fn3 domain is an Fn3 domain derived from the wild-type tenth module of the human fibronectin type III domain ( 10 Fn3): VSDVPRDLEVVAATPTSLLI SWDAPAVTVR YYRITYGETGGNSPVQEFTV PGSKST AT ISGLKPGVDYTITVYAV TGRGDSPASSKP ISINYRT (SEQ ID NO: 4) (BC, DE, and FG loops are underlined).
  • the non-ligand binding sequences of 10 Fn3, i.e., the " 10 Fn3 scaffold” may be altered provided that the 10 Fn3 retains ligand binding function and/or structural stability.
  • a variety of mutant 10 Fn3 scaffolds have been reported. In one aspect, one or more of Asp 7, Glu 9, and Asp 23 is replaced by another amino acid, such as, for example, a non-negatively charged amino acid residue (e.g., Asn, Lys, etc.). These mutations have been reported to have the effect of promoting greater stability of the mutant 10 Fn3 at neutral pH as compared to the wild-type form (see, e.g., PCT Publication No. WO 02/04523 ).
  • Both variant and wild-type 10 Fn3 proteins are characterized by the same structure, namely seven beta-strand domain sequences designated A through G and six loop regions (AB loop, BC loop, CD loop, DE loop, EF loop, and FG loop) which connect the seven beta-strand domain sequences.
  • the beta strands positioned closest to the N- and C-termini may adopt a beta-like conformation in solution.
  • the AB loop corresponds to residues 15-16
  • the BC loop corresponds to residues 21-30
  • the CD loop corresponds to residues 39-45
  • the DE loop corresponds to residues 51-56
  • the EF loop corresponds to residues 60-66
  • the FG loop corresponds to residues 76-87 ( Xu et al., Chemistry & Biology, 9:933-942, 2002 ).
  • the anti-myostatin Adnectin is an 10 Fn3 polypeptide that is at least 40%, 50%, 60%, 65%, 70%, 75%, 80%, 85%, or 90% identical to the human 10 Fn3 domain, shown in SEQ ID NO:4. Much of the variability will generally occur in one or more of the loops.
  • Each of the beta or beta-like strands of a 10 Fn3 polypeptide may consist essentially of an amino acid sequence that is at least 80%, 85%, 90%, 95% or 100% identical to the sequence of a corresponding beta or beta-like strand of SEQ ID NO:4, provided that such variation does not disrupt the stability of the polypeptide in physiological conditions.
  • the invention provides an anti-myostatin Adnectin comprising a tenth fibronectin type III ( 10 Fn3) domain, wherein the 10 Fn3 domain comprises a loop, AB; a loop, BC; a loop, CD; a loop, DE; a loop EF; and a loop FG; and has at least one loop selected from loop BC, DE, and FG with an altered amino acid sequence relative to the sequence of the corresponding loop of the human 10 Fn3 domain.
  • 10 Fn3 domain comprises a loop, AB; a loop, BC; a loop, CD; a loop, DE; a loop EF; and a loop FG; and has at least one loop selected from loop BC, DE, and FG with an altered amino acid sequence relative to the sequence of the corresponding loop of the human 10 Fn3 domain.
  • the anti-myostatin Adnectins of the present invention comprise an 10 Fn3 domain comprising an amino acid sequence at least 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to the non-loop regions of SEQ ID NO:4, wherein at least one loop selected from BC, DE, and FG is altered.
  • the BC and FG loops are altered, and in some embodiments, the BC, DE, and FG loops are altered, i.e., the 10 Fn3 domains comprise non-naturally occurring loops.
  • the AB, CD and/or the EF loops are altered.
  • altered is meant one or more amino acid sequence alterations relative to a template sequence (corresponding human fibronectin domain) and includes amino acid additions, deletions, substitutions or a combination thereof. Altering an amino acid sequence may be accomplished through intentional, blind, or spontaneous sequence variation, generally of a nucleic acid coding sequence, and may occur by any technique, for example, PCR, error-prone PCR, or chemical DNA synthesis.
  • one or more loops selected from BC, DE, and FG may be extended or shortened in length relative to the corresponding human fibronectin loop.
  • the length of the loop may be extended by 2-25 amino acids.
  • the length of the loop may be decreased by 1-11 amino acids.
  • the length of a loop of 10 Fn3 may be altered in length as well as in sequence to obtain the greatest possible flexibility and affinity in antigen binding.
  • the polypeptide comprises a Fn3 domain that comprises an amino acid sequence at least 80, 85, 90, 95, 98, 99, or 100% identical to the non-loop regions of SEQ ID NO: 4, wherein at least one loop selected from BC, DE, and FG is altered.
  • the altered BC loop has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid substitutions, up to 1, 2, 3, or 4 amino acid deletions, up to 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 amino acid insertions, or a combination thereof.
  • the altered DE loop has up to 1, 2, 3, 4, 5, or 6 amino acid substitutions, up to 1, 2, 3, or 4 amino acid deletions, up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, or 13 amino acid insertions, or a combination thereof.
  • the FG loop has up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, or 12 amino acid substitutions, up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or 11 amino acid deletions, up to 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16 ,17 ,18 ,19, 20, 21, 22, 23, 24, or 25 amino acid insertions, or a combination thereof.
  • the anti-myostatin Adnectins of the invention are based on an 10 Fn3 scaffold and are defined generally by the following sequence: EVVAAT(Z) a SLLI(Z) x YYRITYGE(Z) b QEFTV(Z) y ATI(Z) c DYTITVYAV(Z) z ISINYRT (SEQ ID NO: 5), wherein the AB loop is represented by (Z) a , the CD loop is represented by (Z) b , the EF loop is represented by(Z) e , the BC loop is represented by (Z) x , the DE loop is represented by (Z) y , and the FG loop is represented by (Z) z .
  • Z represents any amino acid and the subscript following the Z represents an integer of the number of amino acids.
  • a may be anywhere from 1-15, 2-15, 1-10, 2-10, 1-8, 2-8, 1-5, 2-5, 1-4, 2-4, 1-3, 2-3, or 1-2 amino acids; and b, c, x, y and z may each independently be anywhere from 2-20, 2-15, 2-10, 2-8, 5-20, 5-15, 5-10, 5-8, 6-20, 6-15, 6-10, 6-8, 2-7, 5-7, or 6-7 amino acids.
  • a is 2 amino acids
  • b is 7 amino acids
  • c is 7 amino acids
  • x 11 amino acids
  • y 6 amino acids
  • z is 12 amino acids.
  • the sequences of the beta strands may have anywhere from 0 to 10, from 0 to 8, from 0 to 6, from 0 to 5, from 0 to 4, from 0 to 3, from 0 to 2, or from 0 to 1 substitutions, deletions or additions across all 7 scaffold regions relative to the corresponding amino acids shown in SEQ ID NO: 4.
  • the sequences of the beta strands may have anywhere from 0 to 10, from 0 to 8, from 0 to 6, from 0 to 5, from 0 to 4, from 0 to 3, from 0 to 2, or from 0 to 1 conservative substitutions across all 7 scaffold regions relative to the corresponding amino acids shown in SEQ ID NO: 4.
  • the core amino acid residues are fixed and any substitutions, conservative substitutions, deletions or additions occur at residues other than the core amino acid residues.
  • the anti-myostatin Adnectins of the invention are based on an 10 Fn3 scaffold and are defined generally by the sequence: wherein the BC loop is represented by (Z) x , the DE loop is represented by (Z) y , and the FG loop is represented by (Z) z .
  • Z represents any amino acid and the subscript following the Z represents an integer of the number of amino acids.
  • x, y and z may each independently be anywhere from 2-20, 2-15, 2-10, 2-8, 5-20, 5-15, 5-10, 5-8, 6-20, 6-15, 6-10, 6-8, 2-7, 5-7, or 6-7 amino acids.
  • x is 11 amino acids
  • y 6 amino acids
  • z is 12 amino acids.
  • the sequences of the beta strands may have anywhere from 0 to 10, from 0 to 8, from 0 to 6, from 0 to 5, from 0 to 4, from 0 to 3, from 0 to 2, or from 0 to 1 substitutions, deletions or additions across all 7 scaffold regions relative to the corresponding amino acids shown in SEQ ID NO: 1.
  • the sequences of the beta strands may have anywhere from 0 to 10, from 0 to 8, from 0 to 6, from 0 to 5, from 0 to 4, from 0 to 3, from 0 to 2, or from 0 to 1 conservative substitutions across all 7 scaffold regions relative to the corresponding amino acids shown in SEQ ID NO: 4.
  • the core amino acid residues are fixed and any substitutions, conservative substitutions, deletions or additions occur at residues other than the core amino acid residues.
  • an anti-myostatin Adnectin described herein may comprise the sequence as set forth in SEQ ID NO: 5 or 6, wherein at least one of BC, DE, and FG loops as represented by (Z) x , (Z) y , and (Z) z , respectively, are altered.
  • amino acid residues corresponding to residues 21-30, 51-56, and 76-87 of SEQ ID NO: 4 define the BC, DE, and FG loops, respectively.
  • a desired target e.g., myostatin
  • residues 21 (S) and 22 (W) of the BC loop as shown in SEQ ID NO: 1 do not need to be modified for binding to myostatin. That is, 10 Fn3 domains with high affinity binding to myostatin may be obtained by modifying only residues 23-30 of loop BC as shown in SEQ ID NO: 4. This is demonstrated in the BC loops exemplified in Table 1, which indicates that only the underlined positions are modified.
  • positions 51 (P) and 56 (T) of loop DE as shown in SEQ ID NO: 4 do not need to be modified for binding myostatin. That is, 10 Fn3 domains with high affinity binding to myostatin may be obtained by modifying only residues 52-55 of loop DE as shown in SEQ ID NO: 4. This is demonstrated in the DE loops exemplified in Table 1, which indicates that only resides spanning the underlined positions were altered.
  • positions 76 (T) and 87 (P) of the FG loop as shown in SEQ ID NO: 1 do not need to be modified for binding myostatin. That is, 10 Fn3 domains with high affinity binding to myostatin may be obtained by modifying only residues 77-86 of loop FG as shown in SEQ ID NO: 4. This is demonstrated in the FG loops exemplified in Table 1, which indicates that only the residues spanning the underlined positions were altered.
  • the BC, DE, and FG loop regions of the anti-myostatin Adnectins of the invention can be described according to consensus sequences. These consensus sequences are exemplified by the BC, DE, and FG loops shown in Table 1, and as determined by WebLogo analysis ( Figs. 2-7 ) ( Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator. Genome Research 2004;14:1188-1190 , herein incorporated by reference in its entirety). WebLogo analysis generates an amino acid signature reflecting the frequency of amino acids in each altered position of the BC, DE, or FG loop.
  • the BC loop, (Z) x is defined by the consensus sequence X 1 -L-P-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 , wherein, X 1 is S, T or Y; X 2 is H, Y, N, R, F, G, S or T; X 3 is A, P, Q, S, F, H, N or R; X 4 is G or A; X 5 H, L, R, V, N, D, F, I or K; X 6 is A, L, G, M, F, I or V; and X 7 is H or N.
  • the BC loop comprises an amino acid sequence selected from SEQ ID NOs: 7, 11-21, 23-31, 34, and 36-38. In one embodiment, the BC loop comprises the amino acid set forth in SEQ ID NO. 34.
  • the DE loop, (Z) y is defined by the consensus sequence G-R-G-X 8 , wherein X 8 is V or L.
  • the DE loop comprises an amino acid selected from SEQ ID NOs: 39 and 42.
  • the DE loop comprises the amino acid set forth in SEQ ID NO. 39.
  • the FG loop, (Z) z is defined by consensus sequence X 9 -X 10 -X 11 -X 12 -X 13 -X 14 -X 15 -X 16 -X 17 -X 18 , wherein X 9 is L, V or I; X 10 is T or S; X 11 is K, R, A, G, S, D, H, N, T or P; X 12 is S, T, A, E, H, K or N; X 13 is K, G, Q, D, E, N, T or S; X 14 is V, I, F, L, M, P, T or Y; X 15 is I, L or Y; X 16 is H, I, V, K, L, R, F, G, S or T; X 17 is Y or H; and X 18 is K, M, L, R or V.
  • the FG loop comprises an amino acid sequence selected from SEQ ID NOs: 46, 50-62, 64
  • the BC loop, (Z) x is defined by the consensus sequence X 19 -X 20 -P-X 21 -G-X 22 -A, wherein X 19 is D, E, V or W; X 20 is A, S or V; X 21 is R, A, G, K or L; and X 22 is L or R.
  • the BC loop comprises an amino acid sequence selected from SEQ ID NOs: 8-10, 22, 32, 33, and 35.
  • the DE loop, (Z) y is defined by the consensus sequence X 23 -G-R-G-X 24 , wherein X 23 is V, P, F, I or L; and X 24 is S, N or T.
  • the DE loop comprises and amino acid sequence selected from SEQ ID NOs: 40, 41, and 43-45.
  • the FG loop, (Z) z is defined by the consensus sequence X 25 -X 26 -R-X 27 -G-X 28 -X 29 -X 30 -X 31 -X 32 , wherein X 25 is I or V; X 26 is F, D or Y; X 27 is D or T; X 28 is P, M, V or T; X 29 is V, L, N, R or S; X 30 is H, T, L, N, Q or S; X 31 is F, W, Y, H or L; and X 32 is D, A or G.
  • the FG loop comprises an amino acid sequence selected from SEQ ID NOs: 47-49, 63, 73, 74, and 78.
  • the invention provides an anti-myostatin Adnectin comprising a BC loop, (Z) x , having the sequence X 1 -L-P-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 and a DE loop, (Z) y , having the sequence G-R-G-X 8 , as defined above.
  • the BC loop comprises an amino acid sequence selected from SEQ ID NOs: 7, 11-21, 23-31, 34, and 36-38
  • the DE loop comprises an amino acid sequence selected from SEQ ID NOs: 39 and 42.
  • the BC and DE loops comprise the amino acid sequences set forth in SEQ ID NOs: 34 and 39, respectively.
  • the anti-myostatin Adnectin comprises a BC loop, (Z) x , having the sequence X 1 -L-P-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 and an FG loop, (Z) z , having the sequence X 9 -X 10 -X 11 -X 12 -X 13 -X 14 -X 15 -X 16 -X 17 -X 18 , as defined above.
  • the BC loop comprises an amino acid sequence selected from SEQ ID NOs: 7, 11-21, 23-31, 34, and 36-38
  • the FG loop comprises an amino acid sequence selected from SEQ ID NOs: 46, 50-62, 64-72, 75-77, and 79.
  • the BC and FG loops comprise the amino acid sequences set forth in SEQ ID NOs: 34 and 75, respectively.
  • the anti-myostatin Adnectin comprises a DE loop, (Z) y , having the sequence G-R-G-X 8 and an FG loop, (Z) z , having the sequence X 9 -X 10 -X 11 -X 12 -X 13 -X 14 -X 15 -X 16 -X 17 -X 18 , as defined above.
  • the DE loop comprises an amino acid sequence selected from SEQ ID NOs: 39 and 42
  • the FG loop comprises an amino acid sequence selected from SEQ ID NOs: 46, 50-62, 64-72, 75-77, and 79.
  • the DE and FG loops comprise the amino acid sequences set forth in SEQ ID NOs: 39 and 75, respectively.
  • the anti-myostatin Adnectin comprises a BC loop, (Z) x , having the sequence X 1 -L-P-X 2 -X 3 -X 4 -X 5 -X 6 -X 7 , a DE loop, (Z) y , having the sequence G-R-G-X 8 and an FG loop, (Z) z , having the sequence X 9 -X 10 -X 11 -X 12 -X 13 -X 14 -X 15 -X 16 -X 17 -X 18 , as defined above.
  • the BC loop comprises an amino acid sequence selected from SEQ ID NOs: 7, 11-21, 23-31, 34, and 36-38
  • the DE loop comprises an amino acid sequence selected from SEQ ID NOs: 39 and 42
  • the FG loop comprises an amino acid sequence selected from SEQ ID NOs: 46, 50-62, 64-72, 75-77, and 79.
  • the BC, DE, and FG loops comprise the amino acid sequences set forth in SEQ ID NOs: 34, 39, and 75, respectively.
  • the invention provides an anti-myostatin Adnectin comprising a BC loop, (Z) x , having the sequence X 19 -X 20 -P-X 21 -G-X 22 -A and a DE loop, (Z) y , having the sequence X 23 -G-R-G-X 24 , as defined above.
  • the BC loop comprises an amino acid sequence selected from SEQ ID NOs: 8-10, 22, 32, 33, and 35
  • the DE loop comprises an amino acid sequence selected from SEQ ID NOs: 40, 41, and 43-45.
  • the anti-myostatin Adnectin comprises a BC loop, (Z) x , having the sequence X 19 -X 20 -P-X 21 -G-X 22 -A and an FG loop, (Z) z , having the sequence X 25 -X 26 -R-X 27 -G-X 28 -X 29 -X 30 -X 30 -X 32 , as defined above.
  • the BC loop comprises an amino acid sequence selected from SEQ ID NOs: 8-10, 22, 32, 33, and 35 and the FG loop comprises an amino acid sequence selected from SEQ ID NOs: 47-49, 63, 73, 74, and 78.
  • the anti-myostatin Adnectin comprises a DE loop, (Z) y , having the sequence X 23 -G-R-G-X 24 and an FG loop, (Z) z , having the sequence X 25 -X 26 -R-X 27 -G-X 28 -X 29 -X 30 -X 30 -X 32 , as defined above.
  • the DE loop comprises an amino acid sequence selected from SEQ ID NOs: 40, 41, and 43-45 and the FG loop comprises an amino acid sequence selected from SEQ ID NOs: 47-49, 63, 73, 74, and 78.
  • the anti-myostatin Adnectin comprises a BC loop, (Z) x , having the sequence X 19 -X 20 -P-X 21 -G-X 22 -A, comprises a DE loop, (Z) y , having the sequence X 23 -G-R-G-X 24 and an FG loop, (Z) z , having the sequence X 25 -X 26 -R-X 27 -G-X 28 -X 29 -X 30 -X 30 -X 32 , as defined above.
  • the BC loop comprises an amino acid sequence selected from SEQ ID NOs: 8-10, 22, 32, 33, and 35
  • the DE loop comprises an amino acid sequence selected from SEQ ID NOs: 40, 41, and 43-45
  • the FG loop comprises an amino acid sequence selected from SEQ ID NOs: 47-49, 63, 73, 74, and 78.
  • an anti-myostatin Adnectin of the invention comprises the sequence set forth in SEQ ID NO: 5 or 6, wherein BC, DE and FG loops as represented by (Z) x , (Z) y , and (Z) z , respectively, are replaced with a respective set of BC, DE, and FG loops having the consensus sequences of SEQ ID NOs: 7-38, 39-45, and 46-79, respectively.
  • an anti-myostatin Adnectin of the invention comprises the sequence set forth in SEQ ID NO: 5 or 6, wherein BC, DE and FG loops as represented by (Z) x , (Z) y , and (Z) z , respectively, are replaced with a respective set of BC, DE, and FG loops having sequences at least 75%, 80%, 85%, 90%, 95%, 97%, 98%, or 99% identical to the BC, DE or FG loop sequences of the clones listed in Table 1.
  • an anti-myostatin Adnectin as described herein is defined by SEQ ID NO: 5 and has a respective set of BC, DE and FG loop sequences from any of the clones listed in Table 1.
  • clone 1979_B06 in Table 1 comprises BC, DE, and FG loops as set forth in SEQ ID NOs: 7, 39, and 46, respectively. Therefore, an anti-myostatin Adnectin based on these loops may comprise SEQ ID NO: 5 or 6, wherein (Z) x comprises SEQ ID NO: 7, (Z) y comprises SEQ ID NO: 39, and (Z) z comprises SEQ ID NO: 46.
  • scaffold regions of such anti-myostatin Adnectins may comprise anywhere from 0 to 20, from 0 to 15, from 0 to 10, from 0 to 8, from 0 to 6, from 0 to 5, from 0 to 4, from 0 to 3, from 0 to 2, or from 0 to 1 substitutions, conservative substitutions, deletions or additions relative to the scaffold amino acids residues of SEQ ID NO: 4.
  • Such scaffold modifications may be made, so long as the anti-myostatin Adnectin is capable of binding myostatin with a desired K D .
  • the BC loop of the anti-myostatin Adnectin of the invention comprises an amino acid sequence selected from the group consisting of: SWSLPHAGHVN (SEQ ID NO: 7), SWVSPRGRAR (SEQ ID NO: 8), SWEVPRGLAR (SEQ ID NO: 9), SWWAPLGLAR (SEQ ID NO: 10), SWTLPHAGLAH (SEQ ID NO: 11), SWYLPYPAHMN (SEQ ID NO: 12), SWSLPFAGHLN (SEQ ID NO: 13), SWSLPYSGLAN (SEQ ID NO: 14), SWSLPHAGHAH (SEQ ID NO: 15), SWTLPNFGLIN (SEQ ID NO: 16), SWTLPHAGRAH (SEQ ID NO: 17), SWSLPYAGHLN (SEQ ID NO: 18), SWSLPYAAHMN (SEQ ID NO: 19), SWSLPYPGHLN (SEQ ID NO: 20), SWSLPYAGHAH (SEQ ID NO: 21), SWDAPGGLAR (SEQ ID NO:
  • the BC loop of the anti-myostatin Adnectin of the invention comprises the underlined portion of any one of SEQ ID NOs: 7-38, as shown in Table 1. In one embodiment, the BC loop comprises the underlined portion of SEQ ID NO: 34.
  • the DE loop of the anti-myostatin Adnectin of the invention comprises an amino acid sequence selected from the group consisting of: PGRGVT (SEQ ID NO: 39), PGRGST (SEQ ID NO: 40), LGRGST (SEQ ID NO: 41), PGRGLT (SEQ ID NO: 42), IGRGST (SEQ ID NO: 43), FGRGTT (SEQ ID NO: 44), and VGRGNT (SEQ ID NO: 45).
  • the DE loop of the anti-myostatin Adnectin of the invention comprises the underlined portion of any one of SEQ ID NOs: 39-45, as shown in Table 1.
  • the DE loop comprises the underlined portion of SEQ ID NO: 39.
  • the FG loop of the anti-myostatin Adnectin of the invention comprises an amino acid sequence selected from the group consisting of: TLTKSQMIHYMP (SEQ ID NO: 46), TIYRDGMSHHDP (SEQ ID NO: 47), TVYRDGPLLLAP (SEQ ID NO: 48), TIFRTGMVQYDP (SEQ ID NO: 49), TLTNSEIILYKP (SEQ ID NO: 50), TLTKSQILHHRP (SEQ ID NO: 51), TLTRSKIIHYMP (SEQ ID NO: 52), TLTHSNIIRYVP (SEQ ID NO: 53), TVSSTKVIVYLP (SEQ ID NO: 54), TITKSTIIIYKP (SEQ ID NO: 55), TVTTTSVILYKP (SEQ ID NO: 56), TLTKSQLIHYMP (SEQ ID NO: 57), TLTRSQVIHYMP (SEQ ID NO: 58), TLTKSKIIHYMP (SEQ ID NO: 59), TV
  • the FG loop of the anti-myostatin Adnectin of the invention comprises the underlined portion of any one of SEQ ID NOs: 46-79, as shown in Table 1. In one embodiment, the FG loop comprises the underlined portion of SEQ ID NO: 75.
  • the anti-myostatin Adnectin of the invention comprises one BC loop sequence selected from the BC loop sequences having SEQ ID NOs: 7-38, or the underlined portion of any one of SEQ ID NOs: 7-38, as shown in Table 1; one DE loop sequence selected from the DE loop sequences having SEQ ID NOs: 39-45, or the underlined portion of any one of SEQ ID NOs: 39-45 as shown in Table 1; and one FG loop sequence selected from the FG loop sequences having SEQ ID NOS: 46-79, or the underlined portion of any one of SEQ ID NOS: 46-79 as shown in Table 1.
  • the anti-myostatin Adnectin of the invention comprises a BC, DE and FG loop amino acid sequence at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to of any one of SEQ ID NOs: 7-38, 39-45, and 46-79, respectively.
  • the anti-myostatin Adnectin of the invention comprises a BC, DE and FG loop amino acid sequence at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to the underlined portion of any one of SEQ ID NOS: 7-38, 39-45, and 46-79, respectively, as shown in Table 1.
  • the anti-myostatin Adnectin comprises the amino acid sequence of any one of SEQ ID Nos: 80-123, 228-239, and 252-273 (full length sequences from Tables 2, 5, and 6). In one embodiment, the anti-myostatin Adnectin comprises the amino acid sequence of SEQ ID NO: 273.
  • the anti-myostatin Adnectin comprises an amino acid sequence at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to any one of SEQ ID NOS: 80-123, 228-239, and 252-273.
  • the anti-myostatin Adnectin comprise an amino acid sequence at least 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to the non-BC, DE, and FG loop regions of SEQ ID NOs: 80-123, 228-239, and 252-273.
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively.
  • the anti-myostatin Adnectin comprises an amino acid sequence at least 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or 100% identical to the amino acid sequence set forth in SEQ ID NO: 273 [PRD-1474], SEQ ID NO: 118 [3116_A06], SEQ ID NO: 281 [core Adnectin sequence shared by PRD-1474 and 3116_A06, preceded by a N-terminal extension sequence (GVSDVPRDL) and followed by a C-terminal tail (EI)] or SEQ ID NO: 331 [core Adnectin sequence of PRD-1474 and 3116_A06 without an N-terminal leader sequence or C-terminal tail].
  • the core Adnectin sequence of PRD-1474 and 3116_A06 is set forth below:
  • the anti-myostatin Adnectin of the present invention comprises an amino acid sequence at least 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to the non-BC, DE, and FG loop regions of SEQ ID NO: 118, 273, 281, or 331.
  • the anti-myostatin Adnectin of the invention and disclosed herein can be described in relation to the anti-myostatin Adnectin comprising BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75.
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the BC loop comprises 1, 2, 3, 4, 5, or 6 amino acid substitutions, such as conservative amino acid substitutions.
  • the BC loop is defined by the consensus sequence X 33 -L-P-X 34 -X 35 -X 36 -X 37 -X 38 -X 39 , wherein X 33 is T or Y; X 34 is Y, N, R, F, G, S, or T; X 35 is A, P, S, F, H, N, or R; X 36 is A; X 37 is H, L, R, V, N, D, F, or I; X 38 is L, G, M, F, I, or V; and X 39 is H.
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the DE loop comprises 1 amino acid substitution, such as a conservative amino acid substitution. Accordingly, in some embodiments, the DE loop is defined by the consensus sequence G-R-G-X 40 , wherein X 40 is L.
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively wherein the FG loop comprises 1, 2, 3, 4, 5, 6, 7, or 8 amino acid substitutions, such as conservative amino acid substitutions. Accordingly, in some embodiments, the FG loop is defined by the consensus sequence X 41 -X 42 -X 43 -X 44 -X 45 -X 46 -X 47 -X 48 -X 49 -X 50 .
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the BC loop has 1, 2, 3, 4, 5, or 6 amino acid substitutions, such as conservative amino acid substitutions, and the DE loop has 1 amino acid substitution, such as a conservative amino acid substitution.
  • the BC loop has an amino acid sequence according to the formula X 33 -L-P-X 34 -X 35 -X 36 -X 37 -X 38 -X 39 , wherein X 33 is T or Y; X 34 is Y, N, R, F, G, S, or T; X 35 is A, P, S, F, H, N, or R; X 36 is A; X 37 is H, L, R, V, N, D, F, or I; X 38 is L, G, M, F, I, or V; and X 39 is H, and the DE loop has an amino acid sequence according to the formula G-R-G-X 40 , wherein X 40 is L.
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the BC loop has 1, 2, 3, 4, 5, or 6 amino acid substitutions, such as conservative amino acid substitutions, and the FG loop has 1, 2, 3, 4, 5, 6, 7, or 8 amino acid substitutions, such as conservative amino acid substitutions.
  • the BC loop comprises an amino acid sequence according to the formula X 33 -L-P-X 34 -X 35 -X 36 -X 37 -X 38 -X 39 , wherein X 33 is T or Y; X 34 is Y, N, R, F, G, S, or T; X 35 is A, P, S, F, H, N, or R; X 36 is A; X 37 is H, L, R, V, N, D, F, or I; X 38 is L, G, M, F, I, or V; and X 39 is H, and the FG loop comprises an amino acid sequence according to the formula X 41 -X 42 -X 43 -X 44 -X 45 -X 46 -X 47 -X 48 -X 49 -X 50 , wherein X 41 is L or I; X 42 is S; X 43 is K, R, A, G, S, H, N, T, or P; X 44 is S, A, E,
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein and the DE loop has 1 amino acid substitution, such as a conservative amino acid substitution, and the FG loop has 1, 2, 3, 4, 5, 6, 7, or 8 amino acid substitutions, such as conservative amino acid substitutions.
  • the DE loop comprises an amino acid sequence according to the formula G-R-G-X 40 , wherein X 40 is L, and the FG loop has an amino acid sequence according to the formula X 41 -X 42 -X 43 -X 44 -X 45 -X 46 -X 47 -X 48 -X 49 -X 50 , wherein X 41 is L or I; X 42 is S; X 43 is K, R, A, G, S, H, N, T, or P; X 44 is S, A, E, H, K, or N; X 45 is K, Q, D, E, N, T, or S; X 46 is V, I, F, L, M, P, or T; X 47 is I or Y; X 48 is H, I, V, L, R, F, G, S, or T; X 49 is H; and X 50 is M, L, R, or V.
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, wherein the BC loop has 1, 2, 3, 4, 5, or 6 amino acid substitutions, such as conservative amino acid substitutions, and the DE loop has 1 amino acid substitution, such as a conservative amino acid substitution, and the FG loop has 1, 2, 3, 4, 5, 6, 7, or 8 amino acid substitutions, such as conservative amino acid substitutions.
  • the BC loop comprises an amino acid sequence according to the formula X 33 -L-P-X 34 -X 35 -X 36 -X 37 -X 38 -X 39 , wherein X 33 is T or Y; X 34 is Y, N, R, F, G, S, or T; X 35 is A, P, S, F, H, N, or R; X 36 is A; X 37 is H, L, R, V, N, D, F, or I; X 38 is L, G, M, F, I, or V; and X 39 is H; the DE loop comprises an amino acid sequence according to the formula G-R-G-X 40 , wherein X 40 is L; and the FG loop has an amino acid sequence according to the formula X 41 -X 42 -X 43 -X 44 -X 45 -X 46 -X 47 -X 48 -X 49 -X 50 , wherein X 41 is L or I; X 42 is S; X 43
  • the anti-myostatin Adnectin of the invention comprises the BC, DE, and FG loops as set forth in SEQ ID NOs: 34, 39, and 75, respectively, and has amino acid substitutions in the BC, DE, and FG loops which allow the anti-myostatin Adnectin to maintain binding to myostatin.
  • amino acid substitutions can be determined by, e.g., deep mutational scanning, as described in Example 8.
  • the anti-myostatin Adnectin of the invention comprises a BC loop comprising an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein: X 51 is selected from the group consisting of A, C, D, F, H, I, K, L, N, Q, R, S, T, V, W, and Y; X 52 is selected from the group consisting of L, M, and V; X 53 is selected from the group consisting of A, C, D, E, I, K, L, M, N, P, Q, R, S, T, V, and Y; X 54 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y; X 55 is selected from the group consisting of A, C, D,
  • X 51 is selected from the group consisting of C, F, I, S, V, W, and Y;
  • X 52 is selected from the group consisting of L;
  • X 53 is selected from the group consisting of P;
  • X 54 is selected from the group consisting of C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y;
  • X 55 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y;
  • X 56 is selected from the group consisting of G;
  • X 57 is selected from the group consisting of A, C, G, H, I, K, L, M, N, Q, R, S, V, W, and Y;
  • X 58 is selected from the group consisting of A, G, L, M, and S;
  • X 51 is selected from the group consisting of F, S, and W;
  • X 52 is selected from the group consisting of L;
  • X 53 is selected from the group consisting of P;
  • X 54 is selected from the group consisting of C, F, G, I, K, L, M, N, R, S, T, V, W, and Y;
  • X 55 is selected from the group consisting of A, C, E, F, H, I, K, L, M, P, Q, R, S, T, V, and Y;
  • X 56 is selected from the group consisting of G;
  • X 57 is selected from the group consisting of A, C, H, K, L, M, N, R, V, W, and Y;
  • X 58 is selected from the group consisting of A, G, and L;
  • X 59 is selected from the group consisting of H, N, and Q.
  • the anti-myostatin Adnectin of the invention comprises a DE loop comprising an amino acid sequence according to the formula G-R-G-X 60 , wherein X 60 is A, C, D, E, F, I, K, L, M, N, Q, S, T, and V.
  • X 60 is C, E, I, L, M, Q, T, and V.
  • X 60 is C, E, I, L, M, and V.
  • the anti-myostatin Adnectin of the invention comprises an FG loop comprising an amino acid sequence according to the formula X 61 -X 62 -X 63 -X 64 -X 65 -X 66 -X 67 -X 68 -X 69 -X 70 , wherein X 61 is selected from the group consisting of A, C, F, I, L, M, Q, T, V, W, and Y; X 62 is selected from the group consisting of A, C, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y; X 63 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; X 64 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, P, Q
  • X 61 is selected from the group consisting of A, C, I, L, M, and V;
  • X 62 is selected from the group consisting of C, F, H, I, L, M, Q, R, S, T, V, W, and Y;
  • X 63 is selected from the group consisting of A, C, D, E, F, G, H, I, L, M, N, P, Q, S, T, V, W, and Y;
  • X 64 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y;
  • X 65 is selected from the group consisting of A, D, E, F, G, H, I, L, M, N, Q, S, T, V, W, and Y;
  • X 66 is selected from the group consisting of C, F, I, L, M, P, T, V, W, and Y
  • X 61 is selected from the group consisting of I and V;
  • X 62 is selected from the group consisting of C, F, I, L, M, T, V, W, and Y;
  • X 63 is selected from the group consisting of A, C, D, E, F, G, H, I, L, M, N, Q, S, T, and V;
  • X 64 is selected from the group consisting of A, C, D, F, G, I, L, M, N, Q, S, T, V, W, and Y;
  • X 65 is selected from the group consisting of A, G, S, T, and W;
  • X 66 is selected from the group consisting of F, I, V, W, and Y;
  • X 67 is selected from the group consisting of F, H, I, L, M, V, W, and Y;
  • X 68 is selected from the group consisting of A, C, F, G, I, K, L, M, T,
  • the anti-myostatin Adnectin of the invention comprises BC, DE, and FG loops, wherein the BC loop comprises an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein, X 51 is selected from the group consisting of A, C, D, F, H, I, K, L, N, Q, R, S, T, V, W, and Y; X 52 is selected from the group consisting of L, M, and V; X 53 is selected from the group consisting of A, C, D, E, I, K, L, M, N, P, Q, R, S, T, V, and Y; X 54 is A, C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y; X 55 is selected from the group consisting of A, C, D,
  • the anti-myostatin Adnectin of the invention comprises BC, DE, and FG loops, wherein the BC loop comprises an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein, X 51 is selected from the group consisting of C, F, I, S, V, W, and Y; X 52 is L; X 53 is P; X 54 is selected from the group consisting of C, D, E, F, G, H, I, K, L, M, N, Q, R, S, T, V, W, and Y; X 55 is selected from the group consisting of A, C, D, E, F, G, H, I, K, L, M, N, P, Q, R, S, T, V, W, and Y; X 56 is G; X 57 is selected from the group consisting of A, C, G, H, I, K, L,
  • the anti-myostatin Adnectin of the invention comprises BC, DE, and FG loops, wherein the BC loop comprises an amino acid sequence according to the formula X 51 -X 52 -X 53 -X 54 -X 55 -X 56 -X 57 -X 58 -X 59 , wherein, X 51 is selected from the group consisting of F, S, and W; X 52 is L; X 53 is P; X 54 is selected from the group consisting of C, F, G, I, K, L, M, N, R, S, T, V, W, and Y; X 55 is selected from the group consisting of A, C, E, F, H, I, K, L, M, P, Q, R, S, T, V, and Y; X 56 is G; X 57 is selected from the group consisting of A, C, H, K, L, M, N, R, V, W, and Y; X 58 is selected from the group
  • the anti-myostatin Adnectin is encoded by a nucleic acid sequence as set forth in any one of SEQ ID NOs: 124-167, 240-251, and 284-305 (full length sequences from Tables 2, 5, and 6). In some embodiments, the anti-myostatin Adnectin is encoded by a nucleic acid sequence that is at least 70%, 75%, 80%, 85%, 90%, 95%, 98%, 99% or 100% identical to any one of SEQ ID NOS: 124-167, 240-251, and 284-305.
  • Fibronectin naturally binds certain types of integrins through its integrin-binding motif, "arginine-glycine-aspartic acid" (RGD).
  • the polypeptide comprises a 10 Fn3 domain that lacks the (RGD) integrin binding motif.
  • the integrin binding domain may be removed by altering the RGD sequence by amino acid substitution, deletion or insertion.
  • BC, DE and/or FG loop amino acid sequences identical to the underlined portion of any one of SEQ ID NOS: 7-38, 39-45, and 46-79, respectively, as shown in Table 1, are grafted into non- 10 Fn3 domain protein scaffolds.
  • one or more loop amino acid sequences is exchanged for or inserted into one or more CDR loops of an antibody heavy or light chain or fragment thereof.
  • the protein domain into which one or more amino acid loop sequences are exchanged or inserted includes, but is not limited to, consensus Fn3 domains (Centocor ,US), ankyrin repeat proteins (Molecular Partners AG, Zurich Switzerland), domain antibodies (Domantis, Ltd, Cambridge, MA), single domain camelid nanobodies (Ablynx, Belgium), Lipocalins (e.g., anticalins; Pieris Proteolab AG, Freising, Germany), Avimers (Amgen, CA), affibodies (Affibody AG, Sweden), ubiquitin (e.g., affilins; Scil Proteins GmbH, Halle, Germany), protein epitope mimetics (Polyphor Ltd, Allschwil, Switzerland), helical bundle scaffolds (e.g. alphabodies, Complix, Belgium), Fyn SH3 domains (Covagen AG, Switzerland), or atrimers (Anaphor, Inc., CA).
  • consensus Fn3 domains (Centocor ,US),
  • the SEQ ID NOs of the BC, DE and FG loops of the exemplary anti-myostatin Adnectins of the invention are presented in Table 1.
  • exemplary anti-myostatin monoAdnectins of the invention are presented in Table 2.
  • Table 2 Anti-Myostatin MonoAdnectins Sequence Amino Acid Sequence Nucleic Acid Sequence 1979_B06 also referred to herein as ATI-1133 (Adnectin core 1 sequence having AdNTl (underlined) and AdCT1 (italics) terminal sequence with His6 tag) 2062_G02 also referred to herein as ATI-1134 (Adnectin core 2 sequence having AdNTl (underlined) and AdCT1 (italics) terminal sequence with His6 tag) 2522_C09 (Adnectin core 3 sequence having AdNTl (underlined) and AdCT1 (italics) terminal sequence with His6 tag) 2523_G06 (Adnectin core 4 sequence having AdNTl (underlined) and AdCT1 (italics) terminal sequence with His6 tag) 2524_C11 (Adnectin core 5 sequence having AdNT1 (underlined) and AdCT
  • Adnectins of the invention compete (e.g., cross-compete) for binding to myostatin with the particular anti-myostatin Adnectins described herein.
  • Such competing Adnectins can be identified based on their ability to competitively inhibit binding to myostatin of Adnectins described herein in standard myostatin binding assays.
  • standard ELISA assays can be used in which a recombinant myostatin protein is immobilized on the plate, one of the Adnectins is fluorescently labeled and the ability of non-labeled Adnectins to compete off the binding of the labeled Adnectin is evaluated.
  • a competitive ELISA format can be performed to determine whether two anti-myostatin Adnectins bind overlapping Adnectin binding sites on myostatin.
  • Adnectin #1 is coated on a plate, which is then blocked and washed. To this plate is added either myostatin alone, or myostatin pre-incubated with a saturating concentration of Adnectin #2. After a suitable incubation period, the plate is washed and probed with a polyclonal anti-myostatin antibody, such as a biotinylated goat anti-myostatin polyclonal antibody (R&D Systems), followed by detection with streptavidin-HRP conjugate and standard tetramethylbenzidine development procedures.
  • a polyclonal anti-myostatin antibody such as a biotinylated goat anti-myostatin polyclonal antibody (R&D Systems)
  • the two Adnectins bind independently of one another, and their Adnectin binding sites do not overlap. If, however, the OD signal for wells that received myostatin/Adnectin#2 mixtures is lower than for those that received myostatin alone, then binding of Adnectin #2 is confirmed to block binding of Adnectin #1 to myostatin.
  • Adnectin #1 is immobilized on an SPR chip surface, followed by injections of either myostatin alone or myostatin pre-incubated with a saturating concentration of Adnectin #2. If the binding signal for myostatin/Adnectin#2 mixtures is the same or higher than that of myostatin alone, then the two Adnectins bind independently of one another, and their Adnectin binding sites do not overlap.
  • SPR surface plasmon resonance
  • binding signal for myostatin/Adnectin#2 mixtures is lower than the binding signal for myostatin alone, then binding of Adnectin #2 is confirmed to block binding of Adnectin #1 to myostatin.
  • a feature of these experiments is the use of saturating concentrations of Adnectin #2. If myostatin is not saturated with Adnectin #2, then the conclusions above do not hold. Similar experiments can be used to determine if any two myostatin binding proteins bind to overlapping Adnectin binding sites.
  • Both assays exemplified above may also be performed in the reverse order where Adnectin#2 is immobilized and myostatin -Adnectin#1 are added to the plate.
  • Adnectin #1 and/or #2 can be replaced with a monoclonal antibody and/or soluble receptor-Fc fusion protein.
  • competition can be determined using a HTRF sandwich assay, as described in Example 4.
  • the competing Adnectin is an Adnectin that binds to the same Adnectin binding site on myostatin as a particular anti-myostatin Adnectin described herein.
  • Standard mapping techniques such as protease mapping, mutational analysis, x-ray crystallography and 2-dimensional nuclear magnetic resonance, can be used to determine whether an Adnectin binds to the same Adnectin binding site as a reference Adnectin (see, e.g., Epitope Mapping Protocols in Methods in Molecular Biology, Vol. 66, G. E. Morris, Ed. (1996 )).
  • Candidate competing anti-myostatin Adnectins can inhibit the binding of anti-myostatin Adnectins of the invention to myostatin by at least 50%, at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90%, at least 95%, at least 97%, at least 98%, or at least 99%.
  • the % competition can be determined using the methods described above.
  • molecules that compete with the anti-myostatin Adnectins of the invention need not be an Adnectin, but can be any type of molecule that binds to myostatin, such as, but not limited to, an antibody, a small molecule, a peptide, and the like.
  • Adnectins of the invention bind to a discontinuous Adnectin binding site on myostatin.
  • the polypeptides bind a region within amino acids 55-66 of myostatin (SEQ ID NO: 3).
  • the polypeptides bind a region within amino acids 85-101 of myostatin (SEQ ID NO: 3).
  • the polypeptides bind within two regions, amino acids 85-101 and 55-66, of myostatin (SEQ ID NO: 3).
  • polypeptides of the invention do not compete for binding to myostatin with ActRIIB. In some embodiments, the polypeptides of the invention compete for binding to myostatin with ALK4 and/or ALK5.
  • the anti-myostatin Adnectin molecules of the present invention may be modified to comprise an N-terminal extension sequence and/or a C-terminal extension.
  • an MG sequence may be placed at the N-terminus of the 10 Fn3 defined by SEQ ID NO: 4. The M will usually be cleaved off, leaving a G at the N-terminus.
  • the first 10 amino acids of the anti-myostatin Adnectins shown in Table 2 may be replaced with an alternative N-terminal sequence, referred to herein as N-terminal extensions, as shown in Table 7.
  • an M, G or MG may also be placed N-terminal to any of the N-terminal extensions shown in Table 7.
  • the anti-myostatin Adnectins described herein may also comprise alternative C-terminal tail sequences, referred to herein as C-terminal extension sequences.
  • C-terminal extension sequences may be truncated at the threonine corresponding to T94 of SEQ ID NO: 4 (i.e., truncated after INYRT (SEQ ID NO: 168) portion of the sequence).
  • Such truncated version may be used as therapeutic molecules in the truncated form, or alternative C-terminal extensions may be added after the threonine residue.
  • Exemplary C-terminal extension sequences are shown in Table 7.
  • SEQ ID NOs: 80-123 Exemplary anti-myostatin Adnectins comprising C-terminal extension sequences are shown in Table 2 as SEQ ID NOs: 80-123.
  • SEQ ID NO: 80 (clone 1979_B06) comprises the naturally occurring C-terminal extension EIDKPSQ (SEQ ID NO: 211) followed by a His6 tag (SEQ ID NO: 328).
  • His6 tag SEQ ID NO: 328.
  • the C-terminal extension sequences (also called “tails"), comprise E and D residues, and may be between 8 and 50, 10 and 30, 10 and 20, 5 and 10, and 2 and 4 amino acids in length.
  • tail sequences include ED-based linkers in which the sequence comprises tandem repeats of ED.
  • the tail sequence comprises 2-10, 2-7, 2-5, 3-10, 3-7, 3-5, 3, 4 or 5 ED repeats.
  • the ED-based tail sequences may also include additional amino acid residues, such as, for example: EI, EID, ES, EC, EGS, and EGC.
  • Adnectin tail sequences such as EIDKPSQ (SEQ ID NO: 211), in which residues D and K have been removed.
  • the ED-based tail comprises an E, I or EI residues before the ED repeats.
  • the N- or C-terminal sequences may be combined with known linker sequences (e.g., SEQ ID NO: 181-227 in Table 4) as necessary when designing an anti-myostatin Adnectin fusion molecule.
  • sequences may be placed at the C-terminus of the 10 Fn3 domain to facilitate attachment of a pharmacokinetic moiety.
  • a cysteine containing linker such as GSGC (SEQ ID NO: 189) may be added to the C-terminus to facilitate site directed PEGylation on the cysteine residue.
  • Exemplary anti-myostatin Adnectins comprising a cysteine containing linker are shown in Table 5 as SEQ ID NOs: 228-239.
  • the application provides for anti-myostatin Adnectins further comprising a pharmacokinetic (PK) moiety.
  • PK pharmacokinetic
  • Improved pharmacokinetics may be assessed according to the perceived therapeutic need. Often it is desirable to increase bioavailability and/or increase the time between doses, possibly by increasing the time that a protein remains available in the serum after dosing. In some instances, it is desirable to improve the continuity of the serum concentration of the protein over time (e.g., decrease the difference in serum concentration of the protein shortly after administration and shortly before the next administration).
  • the anti-myostatin Adnectin may be attached to a moiety that reduces the clearance rate of the polypeptide in a mammal (e.g., mouse, rat, or human) by greater than two-fold, greater than three-fold, greater than four-fold or greater than five-fold relative to the unmodified anti-myostatin Adnectin.
  • a mammal e.g., mouse, rat, or human
  • Other measures of improved pharmacokinetics may include serum half-life, which is often divided into an alpha phase and a beta phase. Either or both phases may be improved significantly by addition of an appropriate moiety.
  • the PK moiety may increase the serum half-life of the polypeptide by more than 5, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 150, 200, 400, 600, 800, 1000% or more relative to the Fn3 domain alone.
  • Moieties that slow clearance of a protein from the blood include polyoxyalkylene moieties (e.g., polyethylene glycol), sugars (e.g., sialic acid), and well-tolerated protein moieties (e.g., Fc and fragments and variants thereof, transferrin, or serum albumin).
  • the anti-myostatin Adnectin may also be fused to albumin or a fragment (portion) or variant of albumin as described in U.S. Publication No. 2007/0048282 , or may be fused to one or more serum albumin binding Adnectin, as described herein.
  • PK moieties that can be used in the invention include those described in Kontermann et al., (Current Opinion in Biotechnology 2011;22:868-76 ), herein incorporated by reference.
  • Such PK moieties include, but are not limited to, human serum albumin fusions, human serum albumin conjugates, human serum albumin binders (e.g., Adnectin PKE, AlbudAb, ABD), XTEN fusions, PAS fusions (i.e., recombinant PEG mimetics based on the three amino acids proline, alanine, and serine), carbohydrate conjugates (e.g., hydroxyethyl starch (HES)), glycosylation, polysialic acid conjugates, and fatty acid conjugates.
  • human serum albumin fusions e.g., human serum albumin conjugates, human serum albumin binders (e.g., Adnectin PKE, AlbudAb, ABD), XTEN fusions
  • the invention provides an anti-myostatin Adnectin fused to a PK moiety that is a polymeric sugar.
  • the PK moiety is a polyethylene glycol moiety or an Fc region.
  • the PK moiety is a serum albumin binding protein such as those described in U.S. Publication Nos. 2007/0178082 and 2007/0269422 .
  • the PK moiety is human serum albumin.
  • the PK moiety is transferrin.
  • the anti-myostatin Adnectin comprises polyethylene glycol (PEG).
  • PEG is a well-known, water soluble polymer that is commercially available or can be prepared by ring-opening polymerization of ethylene glycol according to methods well known in the art ( Sandler and Karo, Polymer Synthesis, Academic Press, New York, Vol. 3, pages 138-161 ).
  • PEG polyethylene glycol molecule
  • X is 20 to 2300 and X is H or a terminal modification, e.g., a C 1-4 alkyl.
  • PEG can contain further chemical groups which are necessary for binding reactions, which result from the chemical synthesis of the molecule; or which act as a spacer for optimal distance of parts of the molecule.
  • such a PEG can consist of one or more PEG side-chains which are linked together. PEGs with more than one PEG chain are called multiarmed or branched PEGs. Branched PEGs are described in, for example, European Published Application No. 473084A and U.S. Pat. No. 5,932,462 .
  • One or more PEG molecules may be attached at different positions on the protein, and such attachment may be achieved by reaction with amines, thiols or other suitable reactive groups.
  • the amine moiety may be, for example, a primary amine found at the N-terminus of a polypeptide or an amine group present in an amino acid, such as lysine or arginine.
  • the PEG moiety is attached at a position on the polypeptide selected from the group consisting of: a) the N-terminus; b) between the N-terminus and the most N-terminal beta strand or beta-like strand; c) a loop positioned on a face of the polypeptide opposite the target-binding site; d) between the C-terminus and the most C-terminal beta strand or beta-like strand; and e) at the C-terminus.
  • PEGylation may be achieved by site-directed PEGylation, wherein a suitable reactive group is introduced into the protein to create a site where PEGylation preferentially occurs.
  • the protein is modified to introduce a cysteine residue at a desired position, permitting site-directed PEGylation on the cysteine.
  • Mutations may be introduced into a protein coding sequence to generate cysteine residues. This might be achieved, for example, by mutating one or more amino acid residues to cysteine.
  • Preferred amino acids for mutating to a cysteine residue include serine, threonine, alanine and other hydrophilic residues.
  • the residue to be mutated to cysteine is a surface-exposed residue.
  • Algorithms are well-known in the art for predicting surface accessibility of residues based on primary sequence or a protein.
  • surface residues may be predicted by comparing the amino acid sequences of binding polypeptides, given that the crystal structure of the framework, based on which binding polypeptides are designed and evolved, has been solved (see Himanen et al., Nature 2001;414:933-8 ) and thus the surface-exposed residues identified.
  • PEGylation of cysteine residues may be carried out using, for example, PEG-maleimide, PEG-vinylsulfone, PEG-iodoacetamide, or PEG-orthopyridyl disulfide.
  • the PEG is typically activated with a suitable activating group appropriate for coupling to a desired site on the polypeptide.
  • PEGylation methods are well-known in the art and further described in Zalipsky, S., et al., "Use of Functionalized Poly(Ethylene Glycols) for Modification of Polypeptides" in Polyethylene Glycol Chemistry: Biotechnical and Biomedical Applications, J. M. Harris, Plenus Press, New York (1992 ), and in Zalipsky (1995) Advanced Drug Reviews 16: 157-182 .
  • PEG may vary widely in molecular weight and may be branched or linear. Typically, the weight-average molecular weight of PEG is from about 100 Daltons to about 150,000 Daltons. Exemplary weight-average molecular weights for PEG include about 20,000 Daltons, about 40,000 Daltons, about 60,000 Daltons and about 80,000 Daltons. In certain embodiments, the molecular weight of PEG is 40,000 Daltons. Branched versions of PEG having a total molecular weight of any of the foregoing can also be used. In some embodiments, the PEG has two branches. In other embodiments, the PEG has four branches. In another embodiment, the PEG is a bis-PEG (NOF Corporation, DE-200MA), in which two Adnectins are conjugated (see, e.g., Example 1 and ATI-1341 of Table 5).
  • the PEGylated anti-myostatin Adnectins will preferably retain at least about 25%, 50%, 60%, 70%, 80%, 85%, 90%, 95% or 100% of the biological activity associated with the unmodified anti-myostatin Adnectin.
  • biological activity refers to its ability to bind to myostatin, as assessed by K D , k on , or k off .
  • the PEGylated anti-myostatin Adnectin shows an increase in binding to myostatin relative to unPEGylated anti-myostatin Adnectin.
  • PEG-modified anti-myostatin Adnectins are shown in Table 5.
  • the anti-myostatin Adnectin is fused to an immunoglobulin Fc domain, or a fragment or variant thereof.
  • a "functional Fc region” is an Fc domain or fragment thereof which retains the ability to bind FcRn.
  • a functional Fc region binds to FcRn, bud does not possess effector function.
  • the ability of the Fc region or fragment thereof to bind to FcRn can be determined by standard binding assays known in the art.
  • the Fc region or fragment thereof binds to FcRn and possesses at least one "effector function" of a native Fc region.
  • effector functions include C1q binding; complement dependent cytotoxicity (CDC); Fc receptor binding; antibody-dependent cell-mediated cytotoxicity (ADCC); phagocytosis; down regulation of cell surface receptors (e.g., B cell receptor; BCR), etc.
  • Such effector functions generally require the Fc region to be combined with a binding domain (e.g., an anti-myostatin Adnectin) and can be assessed using various assays known in the art for evaluating such antibody effector functions.
  • a “native sequence Fc region” comprises an amino acid sequence identical to the amino acid sequence of an Fc region found in nature.
  • a “variant Fc region” comprises an amino acid sequence which differs from that of a native sequence Fc region by virtue of at least one amino acid modification.
  • the variant Fc region has at least one amino acid substitution compared to a native sequence Fc region or to the Fc region of a parent polypeptide, e.g., from about one to about ten amino acid substitutions, and preferably from about one to about five amino acid substitutions in a native sequence Fc region or in the Fc region of the parent polypeptide.
  • the variant Fc region herein will preferably possess at least about 80% sequence identity with a native sequence Fc region and/or with an Fc region of a parent polypeptide, and most preferably at least about 90% sequence identity therewith, more preferably at least about 95% sequence identity therewith.
  • the Fc domain is derived from an IgG1 subclass, however, other subclasses (e.g., IgG2, IgG3, and IgG4) may also be used. Shown below is the sequence of a human IgG1 immunoglobulin Fc domain:
  • the core hinge sequence is underlined, and the CH2 and CH3 regions are in regular text. It should be understood that the C-terminal lysine is optional.
  • the fusion may be formed by attaching an anti-myostatin Adnectin to either end of the Fc molecule, i.e., Fc-anti-myostatin Adnectin or anti-myostatin Adnectin-Fc arrangements.
  • Fc and anti-myostatin Adnectin are fused via a linker.
  • linker sequences include GAGGGGSG (SEQ ID NO: 181), EPKSSD (SEQ ID NO: 182), D, ESPKAQASSVPTAQPQAEGLA (SEQ ID NO: 183), ELQLEESAAEAQDGELD (SEQ ID NO: 184), GQPDEPGGS (SEQ ID NO: 185), GGSGSGSGSGS (SEQ ID NO: 186), ELQLEESAAEAQEGELE (SEQ ID NO: 187), GSGSG (SEQ ID NO: 188), GSGC (SEQ ID NO: 189), AGGGGSG (SEQ ID NO: 190), GSGS (SEQ ID NO: 191), QPDEPGGS (SEQ ID NO: 192), GSGSGS (SEQ ID NO: 193), TVAAPS (SEQ ID NO: 194), KAGGGGSG (SEQ ID NO: 195), KGSGSGSGSGS (SEQ ID NO: 196), KQPDEPGGS (SEQ ID NO: 195), K
  • the Fc region used in the anti-myostatin Adnectin fusion comprises the hinge region of an Fc molecule.
  • the "hinge” region comprises the core hinge residues spanning positions 1-16 of SEQ ID NO: 169 (DKTHTCPPCPAPELLG; SEQ ID NO: 170) of the IgG1 Fc region.
  • the anti-myostatin Adnectin-Fc fusion adopts a multimeric structure (e.g., dimer) owing, in part, to the cysteine residues at positions 6 and 9 of SEQ ID NO: 169 within the hinge region.
  • the hinge region as used herein may further include residues derived from the CH1 and CH2 regions that flank the core hinge sequence, as shown in SEQ ID NO: 169.
  • the hinge sequence is GSTHTCPPCPAPELLG (i.e., hinge sequence for PRD-932; SEQ ID NO: 180).
  • the hinge sequence may include substitutions that confer desirable pharmacokinetic, biophysical, and/or biological properties.
  • Some exemplary hinge sequences include EPKSS DKTHTCPPCPAPELLG GPS (SEQ ID NO: 171; core hinge region underlined), EPKSS DKTHTCPPCPAPELLG GSS (SEQ ID NO 172; core hinge region underlined), EPKSS GSTHTCPPCPAPELLG GSS (SEQ ID NO: 173; core hinge region underlined), DKTHTCPPCPAPELLG GPS (SEQ ID NO: 174; core hinge region underlined), and DKTHTCPPCPAPELLG GSS (SEQ ID NO: 175; core hinge region underlined).
  • the residue P at position 18 of SEQ ID NO: 169 has been replaced with S to ablate Fc effector function; this replacement is exemplified in hinges having any one of SEQ ID NOs: 172, 173, and 175.
  • the residues DK at positions 1-2 of SEQ ID NO: 169 have been replaced with GS to remove a potential clip site; this replacement is exemplified in SEQ ID NO: 173.
  • the C at position 103 of SEQ ID NO: 176 which corresponds to the heavy chain constant region of human IgG1 (i.e., domains CH1-CH3), has been replaced with S to prevent improper cysteine bond formation in the absence of a light chain; this replacement is exemplified in SEQ ID NOs: 171-173.
  • an anti-myostatin Adnectin-Fc fusion may have the following configurations: 1) anti-myostatin Adnectin-hinge-Fc or 2) hinge-Fc-anti-myostatin Adnectin. Therefore, any anti-myostatin Adnectin of the present invention can be fused to an Fc region comprising a hinge sequence according to these configurations.
  • a linker may be used to join the anti-myostatin Adnectin to the hinge-Fc moiety, for example, an exemplary fusion protein may have the configuration anti-myostatin Adnectin-linker-hinge-Fc or hinge-Fc-linker-anti-myostatin Adnectin.
  • a leader sequence may be placed at the N-terminus of the fusion polypeptide.
  • a leader sequence such as METDTLLLWVLLLWVPGSTG (SEQ ID NO: 177) may be added to the N-terminus of the fusion molecule. If the fusion is produced in E. coli, the fusion sequence will be preceded by a methionine.
  • the leader sequence is in bold, the anti-myostatin Adnectin sequence is in italics, and the hinge region is underlined. It should be understood that the C-terminal lysine is optional.
  • the Fc domain comprises the human IgG1 CH2 and CH3 regions as follows: VFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQ YNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLP PSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKL TVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSPGK (SEQ ID NO: 178) and the hinge sequence DKTHTCPPCPAPELLG (SEQ ID NO: 170).
  • the Fc domain comprises the human IgG1 CH2 and CH3 regions as follows: VFLFPPKPKDTLMISRTPEVTCVVVDVSHEDPEVKFNWYVDGVEVHNAKTKPREEQ YNSTYRVVSVLTVLHQDWLNGKEYKCKVSNKALPAPIEKTISKAKGQPREPQVYTLP PSRDELTKNQVSLTCLVKGFYPSDIAVEWESNGQPENNYKTTPPVLDSDGSFFLYSKL TVDKSRWQQGNVFSCSVMHEALHNHYTQKSLSLSP (SEQ ID NO: 179) and the hinge sequence DKTHTCPPCPAPELLG (SEQ ID NO: 170).
  • Adnectin-Fc fusions Exemplary anti-myostatin Adnectin-Fc fusions and Fc-anti-myostatin Adnectin fusions are shown in Table 6 (SEQ ID NOs: 252-273). All sequences may begin with a methionine or a mammalian leader sequence (e.g., SEQ ID NO: 177).
  • the PK moiety is another Adnectin specific, for example, to a serum protein (e.g., human serum albumin), as described in US 2012/0094909 , herein incorporated by reference in its entirety.
  • a serum protein e.g., human serum albumin
  • Other PK moieties that may be used with the Adnectins of the invention are disclosed in Kontermann et al. (Current Opinion in Biotechnology 2011;22:868-76 ), as discussed supra.
  • Adnectin based PK moieties may be directly or indirectly linked to an anti-myostatin Adnectin via a polypeptide linker.
  • Suitable linkers for joining Fn3 domains are those which allow the separate domains to fold independently of each other and form a three dimensional structure that permits high affinity binding to a target molecule.
  • Exemplary polypeptide linkers include PSTSTST (SEQ ID NO: 210), EIDKPSQ (SEQ ID NO: 211), and GS linkers, such as GSGSGSGSGS (SEQ ID NO: 213) and multimers thereof.
  • the linker is a glycine-serine based linker. These linkers comprise glycine and serine residues and may be between 8 and 50, 10 and 30, and 10 and 20 amino acids in length.
  • linkers having an amino acid sequence (GS) 7 (SEQ ID NO: 215), G(GS) 6 (SEQ ID NO: 216), and G(GS) 7 G (SEQ ID NO: 217) include linkers having an amino acid sequence (GS) 7 (SEQ ID NO: 215), G(GS) 6 (SEQ ID NO: 216), and G(GS) 7 G (SEQ ID NO: 217).
  • Other linkers contain glutamic acid, and include, for example, (GSE) 5 (SEQ ID NO: 218) and GGSEGGSE (SEQ ID NO: 219).
  • Other exemplary glycine-serine linkers include (GS) 4 (SEQ ID NO: 212), (GGGGS) 7 (SEQ ID NO: 220), (GGGGS) 5 (SEQ ID NO: 221), and (GGGGS) 3 G (SEQ ID NO: 222).
  • the linker is a glycine-proline based linker.
  • linkers comprise glycine and proline residues and may be between 3 and 30, 10 and 30, and 3 and 20 amino acids in length. Examples include linkers having an amino acid sequence (GP) 3 G (SEQ ID NO: 223), (GP) 5 G (SEQ ID NO: 224), and GPG. In other embodiments, the linker may be a proline-alanine based linker having between 3 and 30, 10 and 30, and 3 and 20 amino acids in length. Examples of proline alanine based linkers include, for example, (PA) 3 (SEQ ID NO: 225), (PA) 6 (SEQ ID NO: 226) and (PA) 9 (SEQ ID NO: 227).
  • an anti-myostatin Adnectin is linked, for example, to an anti-HSA Adnectin via a polypeptide linker having a protease site that is cleavable by a protease in the blood or target tissue.
  • a polypeptide linker having a protease site that is cleavable by a protease in the blood or target tissue.
  • Such embodiments can be used to release an anti-myostatin Adnectin for better delivery or therapeutic properties or more efficient production.
  • Additional linkers or spacers may be introduced at the N-terminus or C-terminus of a Fn3 domain between the Fn3 domain and the polypeptide linker.
  • an anti-myostatin Adnectin may be directly or indirectly linked for example, to an anti-HSA Adnectin via a polymeric linker.
  • Polymeric linkers can be used to optimally vary the distance between each component of the fusion to create a protein fusion with one or more of the following characteristics: 1) reduced or increased steric hindrance of binding of one or more protein domains when binding to a protein of interest, 2) increased protein stability or solubility, 3) decreased protein aggregation, and 4) increased overall avidity or affinity of the protein.
  • an anti-myostatin Adnectin is linked, for example, to an anti-HSA Adnectin, via a biocompatible polymer such as a polymeric sugar.
  • the polymeric sugar can include an enzymatic cleavage site that is cleavable by an enzyme in the blood or target tissue. Such embodiments can be used to release an anti-myostatin Adnectin for better delivery or therapeutic properties or more efficient production.
  • the core Adnectin sequence corresponds to the monoAdnectin sequence lacking the N-terminal extension and C-terminal tail sequences.
  • b Adnectins with cysteine mutants have the core Adnectin sequence of the monoAdnectin in the first column, and are preceded by a N-terminal extension sequence (MGVSDVPRDL; SEQ ID NO: 306) and followed by a C-terminal tail (GSGC[Modification]HHHHHH; SEQ ID NO: 326 or EGSGC[Modification]HHHHHH; SEQ ID NO: 327), as shown in Table 5.
  • Adnectins with an Fc moiety on the C-terminus have the core Adnectin sequence of the monoAdnectin in the first column, which is preceded by a N-terminal extension sequence (GVSDVPRDL; SEQ ID NO: 307) and followed by a C-terminal tail (EI), which is followed by a linker sequence (Table 4) and the Fc region sequence, as described in Table 6.
  • GVSDVPRDL N-terminal extension sequence
  • EI C-terminal tail
  • Table 4 linker sequence
  • Adnectins with an Fc moiety on the N-terminus have an Fc region sequence which is preceded by a N-terminal hinge sequence and followed by a linker (Table 4) and the core Adnectin sequence of the monoAdnectin in the first column, which itself is preceded by a N-terminal extension sequence (GVSDVPRDL; SEQ ID NO: 307) and followed by a C-terminal tail (EI), as shown in Table 6.
  • GVSDVPRDL N-terminal extension sequence
  • EI C-terminal tail
  • SEQ ID NOs of exemplary linkers of the invention are presented in Table 4.
  • Table 4 SEQ ID NO.
  • SEQ ID NOs of exemplary Fc-fused anti-myostatin Adnectins of the invention are presented in Table 6.
  • Table 6 Fc-fused Anti-Myostatin Adnectins Sequence Clone Amino Acid Sequence N-terminal domain Linker C-terminal domain Nucleic Acid Sequence PRD-932 GAGGGGSG (SEQ ID NO: 181) PRD-1171 EPKSSD (SEQ ID NO: 182) PRD-1173 D PRD-1174 PRD-1175 GAGGGGSG (SEQ ID NO: 181) PRD-1177 PRD-1178 GQPDEPGGS (SEQ ID NO: 185) PRD-1180 PRD-1284 PRD-1285 PRD-1286 PRD-1287 PRD-1288 PRD-1301 EPKSSD (SEQ ID NO: 182) PRD-1302 EPKSSD (SEQ ID NO: 182) PRD-1303 EPKSSD (SEQ ID NO: 182) PRD-1304 EPKSSD (SEQ ID NO: 182) PRD-1305 EPKSSD (SEQ ID NO: 18
  • the invention provides an Adnectin comprising fibronectin type III domains that binds myostatin.
  • Adnexus a Bristol-Myers Squibb R&D Company.
  • This disclosure utilizes the in vitro expression and tagging technology, termed 'PROfusion' which exploits nucleic acid-protein fusions (RNA- and DNA-protein fusions) to identify novel polypeptides and amino acid motifs that are important for binding to proteins.
  • Nucleic acid-protein fusion technology is a technology that covalently couples a protein to its encoding genetic information.
  • RNA-protein fusion technology and fibronectin-based scaffold protein library screening methods
  • Szostak et al. U.S. Pat. Nos. 6,258,558 , 6,261,804 , 6,214,553 , 6,281,344 , 6,207,446 , 6,518,018 and 6,818,418 ; Roberts et al., Proc. Natl. Acad. Sci., 1997;94:12297-12302 ; and Kurz et al., Molecules, 2000;5:1259-64 , all of which are herein incorporated by reference.
  • Nucleic acids encoding any of the various proteins or polypeptides disclosed herein may be synthesized chemically. Codon usage may be selected so as to improve expression in a cell. Such codon usage will depend on the cell type selected. Specialized codon usage patterns have been developed for E. coli and other bacteria, as well as mammalian cells, plant cells, yeast cells and insect cells. See for example: Mayfield et al., Proc. Natl. Acad. Sci. USA, 100(2):438-442 (Jan. 21, 2003 ); Sinclair et al., Protein Expr. Purif., 26(I):96-105 (October 2002 ); Connell, N.D., Curr. Opin.
  • the DNA encoding the polypeptide is operably linked to suitable transcriptional or translational regulatory elements derived from mammalian, viral, or insect genes.
  • suitable transcriptional or translational regulatory elements include a transcriptional promoter, an optional operator sequence to control transcription, a sequence encoding suitable mRNA ribosomal binding site, and sequences that control the termination of transcription and translation.
  • the ability to replicate in a host, usually conferred by an origin of replication, and a selection gene to facilitate recognition of transformants is additionally incorporated.
  • the proteins described herein may be produced recombinantly not only directly, but also as a fusion polypeptide with a heterologous polypeptide, which is preferably a signal sequence or other polypeptide having a specific cleavage site at the N-terminus of the mature protein or polypeptide.
  • the heterologous signal sequence selected preferably is one that is recognized and processed (i.e., cleaved by a signal peptidase) by the host cell.
  • An exemplary N-terminal leader sequence for production of polypeptides in a mammalian system is: METDTLLLWVLLLWVPGSTG (SEQ ID NO: 177), which is removed by the host cell following expression.
  • the signal sequence is substituted by a prokaryotic signal sequence selected, for example, from the group of the alkaline phosphatase, penicillinase, 1 pp, or heat-stable enterotoxin II leaders.
  • the native signal sequence may be substituted by, e.g., a yeast invertase leader, a factor leader (including Saccharomyces and Kluyveromyces alpha-factor leaders), or acid phosphatase leader, the C. albicans glucoamylase leader, or the signal sequence described in U.S. Pat. No. 5,631,144 .
  • yeast invertase leader a factor leader (including Saccharomyces and Kluyveromyces alpha-factor leaders), or acid phosphatase leader, the C. albicans glucoamylase leader, or the signal sequence described in U.S. Pat. No. 5,631,144 .
  • mammalian signal sequences as well as viral secretory leaders for example, the herpes simplex gD signal, are available.
  • the DNA for such precursor regions may be ligated in reading frame to DNA encoding the protein.
  • Both expression and cloning vectors contain a nucleic acid sequence that enables the vector to replicate in one or more selected host cells.
  • this sequence is one that enables the vector to replicate independently of the host chromosomal DNA, and includes origins of replication or autonomously replicating sequences.
  • origins of replication or autonomously replicating sequences are well known for a variety of bacteria, yeast, and viruses.
  • the origin of replication from the plasmid pBR322 is suitable for most Gram-negative bacteria, the 2 micron plasmid origin is suitable for yeast, and various viral origins (SV40, polyoma, adenovirus, VSV or BPV) are useful for cloning vectors in mammalian cells.
  • the origin of replication component is not needed for mammalian expression vectors (the SV40 origin may typically be used only because it contains the early promoter).
  • Selection genes may contain a selection gene, also termed a selectable marker.
  • Typical selection genes encode proteins that (a) confer resistance to antibiotics or other toxins, e.g., ampicillin, neomycin, methotrexate, or tracycline, (b) complement auxotrophic deficiencies, or (c) supply critical nutrients not available from complex media, e.g., the gene encoding D-alanine racemase for Bacilli.
  • Expression and cloning vectors usually contain a promoter that is recognized by the host organism and is operably linked to the nucleic acid encoding the protein of the invention, e.g., a fibronectin-based scaffold protein.
  • Promoters suitable for use with prokaryotic hosts include the phoA promoter, beta-lactamase and lactose promoter systems, alkaline phosphatase, a tryptophan (trp) promoter system, and hybrid promoters such as the tan promoter.
  • trp tryptophan
  • Promoters for use in bacterial systems also will contain a Shine-Dalgarno (S.D.) sequence operably linked to the DNA encoding the protein of the invention.
  • Promoter sequences are known for eukaryotes. Virtually all eukaryotic genes have an AT-rich region located approximately 25 to 30 bases upstream from the site where transcription is initiated. Another sequence found 70 to 80 bases upstream from the start of transcription of many genes is a CNCAAT region where N may be any nucleotide. At the 3' end of most eukaryotic genes is an AATAAA sequence that may be the signal for addition of the poly A tail to the 3' end of the coding sequence. All of these sequences are suitably inserted into eukaryotic expression vectors.
  • suitable promoting sequences for use with yeast hosts include the promoters for 3-phosphoglycerate kinase or other glycolytic enzymes, such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triosephosphate isomerase, phosphoglucose isomerase, and glucokinase.
  • 3-phosphoglycerate kinase or other glycolytic enzymes such as enolase, glyceraldehyde-3-phosphate dehydrogenase, hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate
  • Transcription from vectors in mammalian host cells can be controlled, for example, by promoters obtained from the genomes of viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and most preferably Simian Virus 40 (SV40), from heterologous mammalian promoters, e.g., the actin promoter or an immunoglobulin promoter, from heat-shock promoters, provided such promoters are compatible with the host cell systems.
  • viruses such as polyoma virus, fowlpox virus, adenovirus (such as Adenovirus 2), bovine papilloma virus, avian sarcoma virus, cytomegalovirus, a retrovirus, hepatitis-B virus and most preferably Simian Virus 40 (SV
  • Enhancer sequences are now known from mammalian genes (globin, elastase, albumin, ⁇ -fetoprotein, and insulin). Typically, however, one will use an enhancer from a eukaryotic cell virus. Examples include the SV40 enhancer on the late side of the replication origin (bp 100-270), the cytomegalovirus early promoter enhancer, the polyoma enhancer on the late side of the replication origin, and adenovirus enhancers.
  • the enhancer may be spliced into the vector at a position 5' or 3' to the peptide-encoding sequence, but is preferably located at a site 5' from the promoter.
  • Expression vectors used in eukaryotic host cells will also contain sequences necessary for the termination of transcription and for stabilizing the mRNA. Such sequences are commonly available from the 5' and, occasionally 3', untranslated regions of eukaryotic or viral DNAs or cDNAs. These regions contain nucleotide segments transcribed as polyadenylated fragments in the untranslated portion of mRNA encoding the protein of the invention.
  • One useful transcription termination component is the bovine growth hormone polyadenylation region. See WO 94/11026 and the expression vector disclosed therein.
  • the recombinant DNA can also include any type of protein tag sequence that may be useful for purifying the protein.
  • protein tags include, but are not limited to, a histidine tag, a FLAG tag, a myc tag, an HA tag, or a GST tag.
  • Appropriate cloning and expression vectors for use with bacterial, fungal, yeast, and mammalian cellular hosts can be found in Cloning Vectors: A Laboratory Manual, (Elsevier, New York (1985 )), the relevant disclosure of which is hereby incorporated by reference.
  • the expression construct is introduced into the host cell using a method appropriate to the host cell, as will be apparent to one of skill in the art.
  • a variety of methods for introducing nucleic acids into host cells are known in the art, including, but not limited to, electroporation; transfection employing calcium chloride, rubidium chloride, calcium phosphate, DEAE-dextran, or other substances; microprojectile bombardment; lipofection; and infection (where the vector is an infectious agent).
  • Suitable host cells include prokaryotes, yeast, mammalian cells, or bacterial cells.
  • Suitable bacteria include gram negative or gram positive organisms, for example, E. coli or Bacillus spp. Yeast, preferably from the Saccharomyces species, such as S. cerevisiae, may also be used for production of polypeptides.
  • Saccharomyces species such as S. cerevisiae
  • Various mammalian or insect cell culture systems can also be employed to express recombinant proteins. Baculovirus systems for production of heterologous proteins in insect cells are reviewed by Luckow et al. (Bio/Technology, 6:47 (1988 )).
  • suitable mammalian host cell lines include endothelial cells, COS-7 monkey kidney cells, CV-1, L cells, C127, 3T3, Chinese hamster ovary (CHO), human embryonic kidney ceils, HeLa, 293, 293T, and BHK cell lines.
  • Purified polypeptides are prepared by culturing suitable host/vector systems to express the recombinant proteins. For many applications, the small size of many of the polypeptides disclosed herein would make expression in E. coli as the preferred method for expression. The protein is then purified from culture media or cell extracts.
  • the present invention is also directed to cell lines that express an anti-myostatin Adnectin or fusion polypeptide thereof. Creation and isolation of cell lines producing an anti-myostatin Adnectin can be accomplished using standard techniques known in the art, such as those described herein.
  • Host cells are transformed with the herein-described expression or cloning vectors for protein production and cultured in conventional nutrient media modified as appropriate for inducing promoters, selecting transformants, or amplifying the genes encoding the desired sequences.
  • the host cells used for high-throughput protein production (HTPP) and mid-scale production were those from the HMS174-bacterial strain.
  • Adnectins of the present invention can also be obtained in aglycosylated form by producing the Adnectins in, e.g., prokaryotic cells (e.g., E. coli).
  • prokaryotic cells e.g., E. coli
  • aglycosylated forms of the Adnectins of the invention exhibit the same affinity, potency, and mechanism of action as glycosylated Adnectins when tested in vitro.
  • the host cells used to produce the proteins of this invention may be cultured in a variety of media.
  • Commercially available media such as Ham's F10 (Sigma), Minimal Essential Medium ((MEM), (Sigma), RPMI-1640 (Sigma), and Dulbecco's Modified Eagle's Medium ((DMEM), Sigma)) are suitable for culturing the host cells.
  • MEM Minimal Essential Medium
  • RPMI-1640 Sigma
  • DMEM Dulbecco's Modified Eagle's Medium
  • any of these media may be supplemented as necessary with hormones and/or other growth factors (such as insulin, transferrin, or epidermal growth factor), salts (such as sodium chloride, calcium, magnesium, and phosphate), buffers (such as HEPES), nucleotides (such as adenosine and thymidine), antibiotics (such as Gentamycin drug), trace elements (defined as inorganic compounds usually present at final concentrations in the micromolar range), and glucose or an equivalent energy source. Any other necessary supplements may also be included at appropriate concentrations that would be known to those skilled in the art.
  • the culture conditions such as temperature, pH, and the like, are those previously used with the host cell selected for expression, and will be apparent to the ordinarily skilled artisan.
  • Proteins disclosed herein can also be produced using cell-translation systems.
  • the nucleic acids encoding the polypeptide must be modified to allow in vitro transcription to produce mRNA and to allow cell-free translation of the mRNA in the particular cell-free system being utilized (eukaryotic such as a mammalian or yeast cell-free translation system or prokaryotic such as a bacterial cell-free translation system.
  • Proteins of the invention can also be produced by chemical synthesis (e.g., by the methods described in Solid Phase Peptide Synthesis, 2nd Edition, The Pierce Chemical Co., Rockford, Ill. (1984 )). Modifications to the protein can also be produced by chemical synthesis.
  • the proteins of the present invention can be purified by isolation/purification methods for proteins generally known in the field of protein chemistry.
  • Non-limiting examples include extraction, recrystallization, salting out (e.g., with ammonium sulfate or sodium sulfate), centrifugation, dialysis, ultrafiltration, adsorption chromatography, ion exchange chromatography, hydrophobic chromatography, normal phase chromatography, reversed-phase chromatography, get filtration, gel permeation chromatography, affinity chromatography, electrophoresis, countercurrent distribution or any combinations of these.
  • polypeptides may be exchanged into different buffers and/or concentrated by any of a variety of methods known to the art, including, but not limited to, filtration and dialysis.
  • the purified polypeptide is preferably at least 85% pure, or preferably at least 95% pure, and most preferably at least 98% pure. Regardless of the exact numerical value of the purity, the polypeptide is sufficiently pure for use as a pharmaceutical product.
  • Binding of an anti-myostatin Adnectin of the invention to a target molecule may be assessed in terms of equilibrium constants (e.g., dissociation, K D ) and in terms of kinetic constants (e.g., on-rate constant, k on and off-rate constant, k off ).
  • An Adnectin will generally bind to a target molecule with a K D of less than 500 nM, 100 nM, 10 nM, 1 nM, 500 pM, 200 pM, or 100 pM, although higher K D values may be tolerated where the k off is sufficiently low or the k on , is sufficiently high.
  • Anti-myostatin Adnectins that bind to and antagonize myostatin can be identified using various in vitro assays.
  • the assays are high-throughput assays that allow for screening multiple candidate Adnectins simultaneously.
  • BMP-11 which shares 90% amino acid identity with myostatin, can be used as a surrogate for myostatin in in vitro assays when the assay is performed under saturating conditions.
  • anti-myostatin Adnectins fused to Fc domains can bind both myostatin and BMP-11, whereas monoAdnectins bind preferentially to myostatin.
  • bivalent Fc-fused Adnectins may reflect the increased avidity of bivalent Fc-fused Adnectins compared to monovalent Adnectins. Similar enhanced binding to BMP11 is observed with bivalent PEGylated Adnectins, such as ATI-1341, which comprise Adnectins fused to two ends of a 20kDa PEG moiety.
  • Exemplary assays for determining the binding affinity of anti-myostatin Adnectins are described in the Examples infra, and include, but are not limited to, solution phase methods such as the kinetic exclusion assay (KinExA) ( Blake et al., JBC 1996;271:27677-85 ; Drake et al., Anal Biochem 2004;328:35-43 ), surface plasmon resonance (SPR) with the Biacore system (Uppsala, Sweden) ( Welford et al., Opt. Quant.
  • KinExA kinetic exclusion assay
  • SPR surface plasmon resonance
  • biomolecular interactions can be monitored in real time with the Biacore system, which uses SPR to detect changes in the resonance angle of light at the surface of a thin gold film on a glass support due to changes in the refractive index of the surface up to 300 nm away.
  • Biacore analysis generates association rate constants, dissociation rate constants, equilibrium dissociation constants, and affinity constants. Binding affinity is obtained by assessing the association and dissociation rate constants using a Biacore surface plasmon resonance system (Biacore, Inc.).
  • a biosensor chip is activated for covalent coupling of the target. The target is then diluted and injected over the chip to obtain a signal in response units of immobilized material.
  • the anti-myostatin Adnectins of the invention exhibit a K D in the SPR affinity assay described in Example 6 of 500 nM or less, 400 nM or less, 300 nM or less, 200 nM or less, 150 nM or less, 100 nM or less, 90 nM or less, 80 nM or less, 70 nM or less, 60 nM or less, 50 nM or less, 40 nM or less, 30 nM or less, 20 nM or less, 15 nM or less, 10 nM or less, 5 nM or less, or 1 nM or less.
  • the K D is 15 nM or less. More preferably, the K D is 2.0 nM or less.
  • the anti-myostatin Adnectins of the invention exhibit an IC50 in the HTRF assay described in Example 4 of 5 nM or less, 4 nM or less, 3 nM or less, 2.5 nM or less, 2 nM or less, 1.5 nM or less, 1 nM or less, 0.5 nM or less, 0.2 nM or less, or 0.1 nM or less.
  • the IC50 is 1.5 nM or less. More preferably, the IC50 is 0.5 nM or less.
  • the anti-myostatin Adnectins of the invention exhibit K D in the kinetic exclusion assay described in Example 7 of 2 nM or less, 1.5 nM or less, 1 nM or less, 900 pM or less, 850 pM or less, 800 pM or less, 750 pM or less, 700 pM or less, 650 pM or less, 600 pM or less, 550 pM or less, 500 pM or less, 450 pM or less, 400 pM or less, 350 pM or less, 340 pM or less, 330 pM or less, 300 pM or less, 250 pM or less, 200 pM or less, 150 pM or less, or 100 pM or less.
  • the K D is 850 pM or less.
  • the assays described herein above are exemplary, and that any method known in the art for determining the binding affinity between proteins (e.g., fluorescence based-transfer (FRET), enzyme-linked immunosorbent assay, and competitive binding assays (e.g., radioimmunoassays)) can be used to assess the binding affinities of the anti-myostatin Adnectins of the invention.
  • FRET fluorescence based-transfer
  • enzyme-linked immunosorbent assay e.g., enzyme-linked immunosorbent assay
  • competitive binding assays e.g., radioimmunoassays
  • anti-myostatin Adnectins to antagonize myostatin activity can be readily determined using various in vitro assays.
  • the assays are high-throughput assays that allow for screening multiple candidate Adnectins simultaneously.
  • the antagonist effects of anti-myostatin Adnectins on myostatin activity can be determined in cell-based activin responsive element (ARE)-luciferase reporter assays, as described in Example 3.
  • ARE activin responsive element
  • the anti-myostatin Adnectins of the invention decrease myostatin-induced ARE-luciferase activity by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90% or more relative to a control upon co-incubating myostatin with an anti-myostatin Adnectin prior to stimulating cells with the mixture.
  • An exemplary control reaction involves treating cells with myostatin alone or myostatin preincubated with an excess of a benchmark myostatin inhibitor such as Human Activin RIIB Fc Chimera (R&D Systems) or ActRIIb-Fc as described in Morrison et al.
  • the anti-myostatin Adnectins of the invention inhibit ARE-luciferase reporter activity with an IC50 of 500 nM or less, 400 nM or less, 300 nM or less, 200 nM or less, 100 nM or less, 50 nM or less, 10 nM or less, 5 nM or less, 1 nM, 0.5 nM or less, 0.4 nM or less, 0.3 nM or less, 0.2 nM or less, or 0.10 nM or less, as described in Example 3.
  • an IC50 500 nM or less, 400 nM or less, 300 nM or less, 200 nM or less, 100 nM or less, 50 nM or less, 10 nM or less, 5 nM or less, 1 nM, 0.5 nM or less, 0.4 nM or less, 0.3 nM or less, 0.2 nM or less, or 0.10 nM or less, as described in Example 3.
  • the antagonistic effects of anti-myostatin Adnectins on myostatin activity can be determined by measuring the extent of SMAD phosphorylation in myostatin-treated cells, as described in Example 5.
  • the anti-myostatin Adnectins of the invention decrease myostatin-induced SMAD phosphorylation by at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 95%, or at least 97% or more relative to a control upon co-incubating myostatin with an anti-myostatin Adnectin prior to stimulating the cells with the mixture.
  • An exemplary control reaction involves treating cells with myostatin alone or myostatin preincubated with an excess of a benchmark myostatin inhibitor such as Human Activin RIIB Fc Chimera (R&D Systems) or ActRIIb-Fc as described in Morrison et al. (Experimental Neurology 2009;217:258-68 ).
  • a benchmark myostatin inhibitor such as Human Activin RIIB Fc Chimera (R&D Systems) or ActRIIb-Fc as described in Morrison et al.
  • the anti-myostatin Adnectins of the invention inhibit SMAD phosphorylation with an IC50 of 1 nM or less, 0.8 nM or less, 0.6 nM or less, 0.4 nM or less, 0.3 nM or less, 0.2 nM or less, or 0.1 nM or less in a 12-point or 4-point inhibition response, as described in Example 5.
  • the anti-myostatin Adnectins of the invention at 10 nM inhibit SMAD phosphorylation by myostatin by at least 50%, at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, or at least 98% or more, as described in Example 5.
  • in vitro model systems which use cells, tissue culture and histological methods for studying motor neuron disease.
  • a rat spinal cord organotypic slice subjected to glutamate excitotoxicity is useful as a model system to test the effectiveness of anti-myostatin Adnectins in preventing motor neuron degeneration.
  • in vitro systems for use in studying ALS see, e.g., Bar, P. R., Eur. J. Pharmacol. (2000) 405:285 295 ; Silani et al., J. Neurol. (2000) 247 Suppl 1:128 36 ; Martin et al., Int. J. Mol. Med. (2000) 5:3 13 .
  • the assays described herein are exemplary, and that any method known in the art that can serve as a readout for myostatin activity are suitable for use for testing the myostatin antagonizing effects of the anti-myostatin Adnectins of the invention (e.g., real-time RT-PCR of mRNAs of SMAD target genes (e.g., Smad 7; Ciarmela et al., Journal of Clinical Endocrinology & Metabolism 2011;96;755-65 ) or mRNAs of ARE-containing genes).
  • SMAD target genes e.g., Smad 7; Ciarmela et al., Journal of Clinical Endocrinology & Metabolism 2011;96;755-65
  • mRNAs of ARE-containing genes e.g., Smad 7; Ciarmela et al., Journal of Clinical Endocrinology & Metabolism 2011;96;755-65 .
  • non-limiting examples of such animal models include, e.g., the X-linked muscular dystrophy mouse (mdx) model ( US2011/0008375 , Gehrig et al., Nature 2012;484:394-8 ), including 4 additional strains of mdx mouse- mdx 2cv, mdx3cv, mdx4cv, or mdx5cv mouse ( Phelps et al., Human Molecular Genetics. 1996;5(8):1149-1153 ), the mdx mouse with additional ablation of the dystrophin homologue utrophin ( mdx / utr - /- ) ( Deconinck et al., Cell.
  • mdx X-linked muscular dystrophy mouse
  • mice for the study of motoneuron disorders are transgenic mice with an ALS-linked mutant Cu/Zn superoxide dismutase (SOD1) gene (mSOD1G93A and/or mSOD1G37R). These mice develop a dominantly inherited adult-onset paralytic disorder with many of the clinical and pathological features of familial ALS. (e.g., Gurney et al., Science (1994) 264:1772 1775 ; Nagano et al., Life Sci (2002) 72:541 548 ). Other animal models include two naturally occurring murine models for progressive motor neuronopathy (pmn) and wobbler ( Haegggeli and Kato, Neurosci. Lett. (2002) 335:39 43 ).
  • Animal models of other neurodegenerative or neuropathological diseases in addition to ALS include a transgenic mouse model for evaluating spinal and bulbar muscular atrophy (SBMA) ( Katsuno et al., Neuron (2002) 35:843 854 ), animal models for human paralytic poliomyelitis ( Ford et al., Microb. Pathog. (2002) 33:97 107 ), animal models of spinal muscular atrophy ( Schmid et al., J. Child Neurol. 22, 1004-1012, 2007 ), animal models for distal myopathy and hereditary inclusion body myopathy ( Malicdan et al., Acta Myol.
  • SBMA spinal and bulbar muscular atrophy
  • Animal models for testing the efficacy of the anti-myostatin Adnectins of the invention against muscle volume loss due to atrophy and/or inactivity include, but are not limited to, mouse models of unilateral immobilization ( Madaro et al., Basic Applied Myology 2008;18:149-153 ), Achilles tendon laceration (tenotomy) ( Bialek et al., Physiol Genomics 2011;43:1075-86 ), and those disclosed in Powers et al. (Am J Physiol Regul Integr Comp Physiol 2005;288:R337-44 ), such as, hindlimb suspension of animals, limb immobilization, and controlled mechanical ventilation.
  • Non-limiting examples of such animal models include Lep ob/ob mice, Lepr db mice, Kuo Kondo mice, KK/ Ay mice, New Zealand Obese (NZO) mice, NONcNZO10 mice, Tsumara Suzuki Obese Diabetes (TSOD) and Tsumara Suzuki Non Obese (TSNO)mice, M16 mice, Zucker fatty rats, Zucker diabetic fatty rats, SHR/N- cp rat, JCR/LA -cp rats, Otsuka Long Evans Tokushima Fatty rats, Obese rhesus monkeys, Cohen diabetic rats, Goto-Kakizaki rats, and non-obese mutant C57 BL/6 (Akita) mice.
  • Type 2 diabetes can also be induced by diet by, e.g., feeding high fat feed to non-obese, non-diabetic C57BL6 mice ( Surwit et al., Diabetes 1988;37:1163-7 ).
  • Type 2 diabetes can also be chemically induced with, e.g., goldthioglucose ( Le Marchand Houseel et al., Am J Physiol 1978;234:E348-58 ) or streptozotocin, or induced surgically (e.g., partial pancreatomized diabetic animals) ( McNeil JH., Experimental models of diabetes.
  • the efficacy of the anti-myostatin Adnectins of the invention for increasing muscle mass or volume can be tested by subcutaneous injection of mice, as described in Example 9. Given that the inhibition of myostatin increases muscle mass, the anti-myostatin Adnectins of the invention are expected to increase body weight and muscle mass, the extent to which can be used to determine the potency of the Adnectins.
  • the anti-myostatin Adnectins of the invention can be administered to SCID mice, which are unable to mount cellular or humoral immune responses.
  • SCID mice can be crossed with other genetic models, such as those described herein (e.g., diabetic mice), to develop an immunocompromised mouse model amenable to chronic treatment with the anti-myostatin Adnectins of the invention.
  • the present invention provides anti-myostatin Adnectins useful for the treatment of myostatin-related disease or disorders, e.g., muscle wasting disorders, muscle atrophy, metabolic disorders, and bone degenerative disorders. Accordingly, in certain embodiments the invention provides methods for attenuating or inhibiting a myostatin-related disease or disorder in a subject comprising administering an effective amount of myostatin-binding polypeptide, i.e., an anti-myostatin Adnectin, to a subject.
  • the subject is a human.
  • the anti-myostatin Adnectins are pharmaceutically acceptable to a mammal, in particular a human.
  • a "pharmaceutically acceptable" polypeptide refers to a polypeptide that is administered to an animal without significant adverse medical consequences, such as essentially endotoxin free, or very low endotoxin levels.
  • the anti-myostatin Adnectins of the present invention will be administered to a subject in combination (concurrently or separately) with an agent known in the art to be useful for the particular disorder or disease being treated.
  • the target patient population for anti-myostatin Adnectin therapy is one that is not amenable to standard therapy for the disease, disorder, or condition being treated due to, e.g., age, pre-existing conditions, genetic makeup, and/or co-morbidities.
  • the anti-myostatin Adnectins of the invention can serve as alternatives to existing therapies that are associated with substantial side effects (e.g., reproductive performance) or safety concerns.
  • the anti-myostatin Adnectins of the present invention can be used to treat muscular, neurological and metabolic disorders associated with muscle wasting and/or muscle atrophy.
  • myostatin overexpression in vivo induces signs and symptoms characteristic of cachexia, and myostatin binding agents can partially resolve the muscle wasting effect of myostatin ( Zimmers et al., Science 2002;296:1486-8 ).
  • Patients with AIDS also exhibit increased serum levels of myostatin immunoreactive material compared to patients without AIDS or to AIDS patients who do not exhibit weight loss ( Gonzalez-Cadavid et al., PNAS 1998;95:14938-43 ).
  • Exemplary disorders that can be treated according to the methods of the invention include myopathies and neuropathies, including, for example, motor neuron disease, neuromuscular and neurological disorders.
  • anti-myostatin Adnectins can be used to treat inherited myopathies and neuromuscular disorders (e.g., muscular dystrophy ( Gonzalez-Kadavid et al., PNAS, 1998;95:14938-43 ), motor neuron disorders, congenital myopathies, inflammatory myopathies and metabolic myopathies), as well as acquired myopathies (e.g., drug induced myopathy, toxin induced myopathy, infection induced myopathy, paraneoplastic myopathy and other myopathies associated with critical illnesses).
  • inherited myopathies and neuromuscular disorders e.g., muscular dystrophy ( Gonzalez-Kadavid et al., PNAS, 1998;95:14938-43 ), motor neuron disorders, congenital myopathies, inflammatory myopathies and metabolic myopathies
  • acquired myopathies e.g., drug induced myopathy, toxin induced myopathy, infection induced myopathy, paraneoplastic myopathy and other myopathies associated with critical illnesses
  • Such disorders include, but are not limited to, Duchenne's muscular dystrophy, progressive muscular dystrophy, Becker's type muscular dystrophy, Dejerine-Landouzy muscular dystrophy, Erb's muscular dystrophy, Emery Dreifuss muscular dystrophy, limb girdle muscular dystrophy, oculopharyngeal muscular dystrophy (OPMD), facioscapulohumeral muscular dystrophy, congenital muscular dystrophy, infantile neuroaxonal muscular dystrophy, myotonic dystrophy (Steinert's disease), distal muscular dystrophy, nemaline myopathy, familial periodic paralysis, nondystrophic myotonia, periodic paralyses, spinal muscular atrophy, spinal muscular atrophy (SMA), amyotrophic lateral sclerosis (ALS), primary lateral sclerosis (PLS), progressive muscular atrophy (PMA), , distal myopathy, myotubular/centronuclear myopathy, nemaline myopathy, mini core
  • Adnectins include, but are not limited to, rigid spine syndrome, muscle-eye-brain disease, heredity motor and sensory neuropathy, Carcot-Marie-Tooth disease, chronic inflammatory neuropathy, progressive hypertrophic neuropathy, tomaculous neuropathy, lupus, Guillain-Barre syndrome, chronic inflammatory demyelinating polyneuropathy, multiple sclerosis, sarcoidosis, diabetic neuropathy, alcoholic neuropathy, disease related neuropathies (e.g., HIV/AIDS, Lyme disease), toxin related neuropathies (e.g., heavy metal, chemotherapy), compression neuropathies (e.g., tumors, entrapment neuropathy), and neuropathies associated with injury or trauma (e.g., cauda equine syndrome, paraplegia, quadriplegia).
  • rigid spine syndrome e.g., muscle-eye-brain disease, heredity motor and sensory neuropathy
  • Carcot-Marie-Tooth disease chronic inflammatory neuropathy, progressive hypertrophic neuropathy, to
  • the anti-myostatin Adnectins of the invention can be used to treat muscular dystrophies (e.g., Duchenne's muscular dystrophy, Becker's type muscular dystrophy), ALS, and sarcopenia.
  • muscular dystrophies e.g., Duchenne's muscular dystrophy, Becker's type muscular dystrophy
  • ALS e.g., ALS, and sarcopenia.
  • Adnectins of the invention include cachexia, wasting syndrome, sarcopenia, congestive obstructive pulmonary disease, cystic fibrosis (pulmonary cachexia), cardiac disease or failure (cardiac cachexia), cancer, wasting due to AIDS, wasting due to renal failure, renal disease, claudication, cachexia associated with dialysis, uremia, rheumatoid arthritis, muscle injury, surgery, repair of damaged muscle, frailty, disuse atrophy, osteoporosis, osteoarthritis, ligament growth and repair.
  • the methods of the invention can also be used to increase muscle volume in subjects who suffer from muscle atrophy due to disuse.
  • Disuse atrophy may result from numerous causes including any disorder or state which leads to prolonged immobility or disuse, including, but not limited to prolonged bedrest, being wheelchair bound, limb immobilization, unloading of the diaphragm via mechanical ventilation, solid organ transplant, joint replacement, stroke, CNS damage related weakness, spinal cord injury, recovery from severe burn, sedentary chronic hemodialysis, post-trauma recovery, post-sepsis recovery and exposure to microgravity ( Powers et al., Am J Physiol Regul Integr Comp Physiol 2005;288:R337-44 ).
  • age-related increases in fat to muscle ratios, and age-related muscular atrophy appear to be related to myostatin.
  • the average serum myostatin-immunoreactive protein increased with age in groups of young (19-35 yr old), middle-aged (36-75 yr old), and elderly (76-92 yr old) men and women, while the average muscle mass and fat-free mass declined with age in these groups ( Yarasheski et al. J Nutr Aging 6(5):343-8 (2002 )).
  • Subjects with muscle atrophy due to aging, and/or subjects who are frail due to, for example, sarcopenia would also benefit from treatment with the anti-myostatin Adnectins of the invention.
  • anti-myostatin Adnectins are also contemplated.
  • anti-myostatin Adnectins would be expected to effectively increase muscle mass and reducing fat in any agriculturally important species, for example, but not limited to, cattle, chicken, turkeys, and pigs.
  • the efficacy of the anti-myostatin Adnectin in the treatment of muscle wasting disorders or muscle atrophy can be determined, for example, by one or more methods for measuring an increase in muscle mass or volume, an increase in the number of muscle cells (hyperplasia), an increase in muscle cell size (hypertrophy) and/or an increase in muscle strength.
  • the muscle volume increasing effects of the anti-myostatin Adnectins of the present invention are demonstrated in the Examples described infra. Methods for determining "increased muscle mass" are well known in the art.
  • muscle content can be measured before and after administration of an anti-myostatin Adnectin of the invention using standard techniques, such as underwater weighing (see, e.g., Bhasin et al.
  • An increase in muscle size may be evidenced by weight gain of at least about 5-10%, preferably at least about 10-20% or more.
  • the anti-myostatin Adnectins of the present invention are useful for treating metabolic disorders, such as obesity, type II diabetes mellitus, diabetes associated disorders, metabolic syndrome, and hyperglycemia.
  • Myostatin is involved in the pathogenesis of type II diabetes mellitus. Myostatin is expressed in adipose tissue and myostatin deficient mice exhibit reduced fat accumulation as they age. Moreover, glucose load, fat accumulation, and total body weight are reduced in myostatin lacking agouti lethal yellow and obese (Lep ob/ob ) mice ( Yen et al., FASEB J. 8:479, 1994 ; McPherron et al., 2002). As disclosed in US2011/0008375 , myostatin antagonists can decrease the fat to muscle ratio in an aged mouse model, preserve skeletal muscle mass and lean body mass, and attenuate kidney hypertrophy in STZ-induced diabetic mice.
  • obesity is a condition in which excess body fat has accumulated to such an extent that health may be negatively affected. It is commonly defined as a body mass index (BMI) of 30 kg/m2 or higher which distinguishes it from being overweight as defined by a BMI of 25 kg/m2 or higher (see, e.g., World Health Organization (2000) (PDF). Technical report series 894: Obesity: Preventing and managing the global epidemic. Geneva: World Health Organization). Excessive body weight is associated with various diseases, particularly cardiovascular diseases, diabetes mellitus type II, obstructive sleep apnea, certain types of cancer, and osteoarthritis.
  • a subject with obesity may be identified, for example, by determining BMI (BMI is calculated by dividing the subject's mass by the square of his or her height), waist circumference and waist-hip ratio (the absolute waist circumference (>102 cm in men and >88 cm in women) and the waist-hip ratio (the circumference of the waist divided by that of the hips of >0.9 for men and >0.85 for women) (see, e.g., Yusuf S, et al., (2004).
  • Body fat percentage measurement techniques include , for example, computed tomography (CT scan), magnetic resonance imaging (MRI), and dual energy X-ray absorptiometry (DEXA).
  • type II diabetes refers to a chronic, life-long disease that results when the body's insulin does not work effectively.
  • a main component of type II diabetes is "insulin resistance,” wherein the insulin produced by the pancreas cannot connect with fat and muscle cells to allow glucose inside to produce energy, causing hyperglycemia (high blood glucose). To compensate, the pancreas produces more insulin, and cells, sensing this flood of insulin, become even more resistant, resulting in a vicious cycle of high glucose levels and often high insulin levels.
  • disorders associated with diabetes refers to conditions and other diseases which are commonly associated with or related to diabetes.
  • disorders associated with diabetes include, for example, hyperglycemia, hyperinsulinaemia, hyperlipidaemia, insulin resistance, impaired glucose metabolism, obesity, diabetic retinopathy, macular degeneration, cataracts, diabetic nephropathy, glomerulosclerosis, diabetic neuropathy, erectile dysfunction, premenstrual syndrome, vascular restenosis, ulcerative colitis, coronary heart disease, hypertension, angina pectoris, myocardial infarction, stroke, skin and connective tissue disorders, foot ulcerations, metabolic acidosis, arthritis, and osteoporosis.
  • the efficacy of the anti-myostatin Adnectins in the treatment of metabolic disorders can be determined, for example, by one or more methods of measuring an increase in insulin sensitivity, an increase in glucose uptake by cells from the subject, a decrease in blood glucose levels, and a decrease in body fat.
  • HbAlc levels can be monitored in subjects having type II diabetes or who are at risk of developing diabetes.
  • the term "hemoglobin 1AC" or "HbAlc” as used herein refers to the product of a non-enzymatic glycation of the hemoglobin B chain.
  • the desired target range of HbAlc levels for people with diabetes can be determined from American Diabetes Association (ADA) guidelines, i.e., the Standards of Medical Care in Diabetes ( Diabetes Care 2012;35(Suppl 1):S511-563 ).
  • Current HbAlc target levels are generally ⁇ 7.0% for people with diabetes, and people who do not have diabetes typically have HbAlc values of less than 6%. Accordingly, the efficacy of the anti-myostatin Adnectins of the present invention can be determined by an observed decrease in the HBAlc level in a subject.
  • the methods of the invention further include administration of an anti-myostatin Adnectin alone, or in combination with other agents that are known in the art for glycemic control (e.g., insulin, GLP1) or for treating art-recognized diabetes-related complications.
  • an anti-myostatin Adnectin alone, or in combination with other agents that are known in the art for glycemic control (e.g., insulin, GLP1) or for treating art-recognized diabetes-related complications.
  • Myostatin knockout mice exhibit increased muscle mass, as well as increased mineral content and density of the mouse humerus, and increased mineral content of both trabecular and cortical bone at regions where muscles attach ( Hamrick et al. Calcif Tissue Intl 2002;71:63-8 ). This suggests that increasing muscle mass may help improve bone strength and reduce osteoporosis and other degenerative bone diseases.
  • Additional diseases or disorders for which the anti-myostatin Adnectins of the present invention are useful include wound healing, anti-fibrotic disease, Lambert-Eaton Syndrome, and Parkinson's Disease.
  • the anti-myostatin Adnectins provided herein may be employed in combination with antidiabetic agents, anti-hyperglycemic agents, anti-hyperinsulinemic agents, anti-retinopathic agents, anti-neuropathic agents, anti-neurodegenerative agents, anti-nephropathic agents, anti-atherosclerotic agents, anti-ischemic agents, anti-hypertensive agents, anti-obesity agents, anti-dyslipidemic agents, anti-dyslipidemic agents, anti-hyperlipidemic agents, anti-hypertriglyceridemic agents, anti-hypercholesterolemic agents, anti-restenotic agents, anti-pancreatic agents, lipid lowering agents, anorectic agents, memory enhancing agents, anti-dementia agents, or cognition promoting agents, appetite suppressants, neuro- or musculo-restorative treatments, treatments for heart failure, treatments for peripheral arterial disease and anti-inflammatory agents.
  • the antidiabetic agents used in combination with the anti-myostatin Adnectins include, but are not limited to, insulin secretagogues or insulin sensitizers, GPR40 receptor modulators, or other antidiabetic agents. These agents include, but are not limited to, dipeptidyl peptidase IV (DP4) inhibitors (for example, sitagliptin, saxagliptin, alogliptin, vildagliptin and the like), biguanides (for example, metformin, phenformin and the like), sulfonyl ureas (for example, gliburide, glimepiride, glipizide and the like), glucosidase inhibitors (for example, acarbose, miglitol, and the like), PPAR ⁇ agonists such as thiazolidinediones (for example, rosiglitazone, pioglitazone, and the like), PPAR ⁇ /
  • the anti-myostatin Adnectins of the present invention may also be optionally employed in combination with one or more hypophagic agents such as diethylpropion, phendimetrazine, phentermine, orlistat, sibutramine, lorcaserin, pramlintide, topiramate, MCHR1 receptor antagonists, oxyntomodulin, naltrexone, Amylin peptide, NPY Y5 receptor modulators, NPY Y2 receptor modulators, NPY Y4 receptor modulators, cetilistat, 5HT2c receptor modulators, and the like.
  • hypophagic agents such as diethylpropion, phendimetrazine, phentermine, orlistat, sibutramine, lorcaserin, pramlintide, topiramate, MCHR1 receptor antagonists, oxyntomodulin, naltrexone, Amylin peptide, NPY Y5 receptor modulators, NPY Y2
  • the anti-myostatin Adnectins of the present invention may also be employed in combination with an agonist of the glucagon-like peptide-1 receptor (GLP-1 R), such as exenatide, liraglutide, GPR-1(1-36) amide, GLP-1 (7-36) amide, GLP-1(7-37) (as disclosed in U.S. Pat. No. 5,614,492 to Habener , the disclosure of which is incorporated herein by reference), which may be administered via injection, intranasally, or by transdermal or buccal devices.
  • GLP-1 R glucagon-like peptide-1 receptor
  • the anti-myostatin Adnectins of the present invention can also be administered with one or more additional therapeutic agents, as appropriate for the particular disease or disorder being treated.
  • additional agents include those that are useful for treating metabolic disorders such as type II diabetes and sarcopenia and include, but are not limited to, GLP-1, GLP-1-like, amylin, and FGF21; those that are useful for treating anti-fibrotic disease, neuromuscular disease, motor neuron disease, and sarcopenia and include, but are not limited to, ghrelin, SARM, Riluzole, testosterone, androgens, growth hormone, hormone replacement therapy, COX-2 inhibitors, troponin activators, ⁇ 2 agonists, CTLA4-Ig (e.g., abetacept, belatacept) and anti-TGF ⁇ antibodies; those that are useful for treating cachexia and other wasting syndromes and include, but are not limited to, TGF ⁇ receptor kinase inhibitors, anti-IL-6, and
  • the anti-myostatin Adnectins of the present invention can be administered with one or more additional agents used in symptomatic therapy.
  • agents for treating the symptoms of ALS include mitochondrial permeability transition (MPT) pore activators , fast skeletal troponin activators, macrophage regulators (e.g., NP001), lysosomal storage disease-treating agents (e.g., NP003), and nicotinic acetylcholine receptor (nAchR) antagonists.
  • MTT mitochondrial permeability transition
  • NP001 macrophage regulators
  • lysosomal storage disease-treating agents e.g., NP003
  • nAchR nicotinic acetylcholine receptor
  • a non-limiting example of an additional agent for use in treating the symptoms of DMD/BMD is an agent that increases ATP levels.
  • the anti-myostatin Adnectins of the present invention can also be administered with one or more additional agents used in disease modification therapy.
  • agents for treating ALS include free radical scavengers (e.g., edaravone (norphenazone), CV-3611), VEGF agonists (e.g., sNN0029), Nogo-A protein I (e.g., GSK122324), SOD1 inhibitors (e.g., ISIS-SOD1Rx), and PGE synthase 1 inhibitors (e.g., AAD-2004).
  • Non-limiting examples of such agents for treating DMD/BMD include those that promote exon skipping (e.g., antisense molecules such as drisapersen (PRO051/GSK2402968), PRO044, Eteplirsen, AVI-4658, AVI-5038, Ataluren (PTC124)), gene therapy agents, anti-inflammatory agents (e.g., CRD007), and anti-fibrotic agents (e.g., HT-100).
  • antisense molecules such as drisapersen (PRO051/GSK2402968), PRO044, Eteplirsen, AVI-4658, AVI-5038, Ataluren (PTC124)
  • gene therapy agents e.g., anti-inflammatory agents (e.g., CRD007), and anti-fibrotic agents (e.g., HT-100).
  • agents that promote exon-skipping can be used in combination with the anti-myostatin Adnectins of the present invention for treating Duchenne's muscular dystrophy and Becker's type muscular dystrophy.
  • specific exons that can be targeted to restore functional dystrophin include exons 7, 8, 17, 43, 44, 45, 46, 50, 51, 52, 53, and 55 (see, e.g., Lu et al., Molecular Therapy 2011;19:9-15 ).
  • more than one agent e.g., antisense oligonucleotides, can be used to induce multi-exon skipping.
  • the present invention further provides pharmaceutical compositions comprising an anti-myostatin Adnectin or fusion proteins thereof described herein, wherein the composition is essentially endotoxin free, or at least contain no more than acceptable levels of endotoxins as determined by the appropriate regulatory agency (e.g., FDA).
  • FDA regulatory agency
  • compositions of the present invention can be in the form of a pill, tablet, capsule, liquid, or sustained release tablet for oral administration; a liquid for intravenous, subcutaneous or parenteral administration; or a gel, lotion, ointment, cream, or a polymer or other sustained release vehicle for local administration.
  • compositions for parenteral administration may, for example, contain excipients, sterile water, saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated napthalenes.
  • excipients sterile water, saline, polyalkylene glycols such as polyethylene glycol, oils of vegetable origin, or hydrogenated napthalenes.
  • Biocompatible, biodegradable lactide polymer, lactide/glycolide copolymer, or polyoxyethylene-polyoxypropylene copolymers may be used to control the release of the compounds.
  • Nanoparticulate compositions may be used to control the biodistribution of the compounds.
  • Other potentially useful parenteral delivery systems include ethylene-vinyl acetate copolymer particles, osmotic pumps, implantable infusion systems, and liposomes.
  • concentration of the compound in the composition varies depending upon a number of factors, including the dosage of the drug to be administered, and the route of administration.
  • Acceptable carriers, excipients, or stabilizers are nontoxic to recipients at the dosages and concentrations employed, and include buffers such as phosphate, citrate, and other organic acids; antioxidants including ascorbic acid and methionine; preservatives (such as octadecyldimethylbenzyl ammonium chloride; hexamethonium chloride; benzalkonium chloride, benzethonium chloride; phenol, butyl or benzyl alcohol; alkyl parabens such as methyl or propyl paraben; catechol; resorcinol; cyclohexanol; 3-pentanol; and m-cresol); low molecular weight (less than about 10 residues) polypeptides; proteins, such as serum albumin, gelatin, or immunoglobulins; hydrophilic polymers such as polyvinylpyrrolidone; amino acids such as glycine, glutamine, asparagine, histidine,
  • the polypeptides of the present invention may be optionally administered as a pharmaceutically acceptable salt, such as non-toxic acid addition salts or metal complexes that are commonly used in the pharmaceutical industry.
  • acid addition salts include organic acids such as acetic, lactic, pamoic, maleic, citric, malic, ascorbic, succinic, benzoic, palmitic, suberic, salicylic, tartaric, methanesulfonic, toluenesulfonic, or trifluoroacetic acids or the like; polymeric acids such as tannic acid, carboxymethyl cellulose, or the like; and inorganic acid such as hydrochloric acid, hydrobromic acid, sulfuric acid phosphoric acid, or the like.
  • Metal complexes include zinc, iron, and the like.
  • the polypeptide is formulated in the presence of sodium acetate to increase thermal stability.
  • the active ingredients may also be entrapped in a microcapsule prepared, for example, by coacervation techniques or by interfacial polymerization, for example, hydroxymethylcellulose or gelatin-microcapsule and poly-(methylmethacylate) microcapsule, respectively, in colloidal drug delivery systems (for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules) or in macroemulsions.
  • colloidal drug delivery systems for example, liposomes, albumin microspheres, microemulsions, nano-particles and nanocapsules
  • Sustained-release preparations may be prepared. Suitable examples of sustained-release preparations include semipermeable matrices of solid hydrophobic polymers containing the proteins of the invention, which matrices are in the form of shaped articles, e.g., films, or microcapsule. Examples of sustained-release matrices include polyesters, hydrogels (for example, poly(2-hydroxyethyl-methacrylate), or poly(vinylalcohol)), polylactides ( U.S. Pat. No.
  • copolymers of L-glutamic acid and y ethyl-L-glutamate non-degradable ethylene-vinyl acetate
  • degradable lactic acid-glycolic acid copolymers such as the LUPRON DEPOTTM (injectable microspheres composed of lactic acid-glycolic acid copolymer and leuprolide acetate)
  • poly-D-(-)-3-hydroxybutyric acid While polymers such as ethylene-vinyl acetate and lactic acid-glycolic acid enable release of molecules for over 100 days, certain hydrogels release proteins for shorter time periods.
  • encapsulated proteins of the invention may remain in the body for a long time, they may denature or aggregate as a result of exposure to moisture at 37°C, resulting in a loss of biological activity and possible changes in immunogenicity.
  • Rational strategies can be devised for stabilization depending on the mechanism involved. For example, if the aggregation mechanism is discovered to be intermolecular S-S bond formation through thio-disulfide interchange, stabilization may be achieved by modifying sulfhydryl residues, lyophilizing from acidic solutions, controlling moisture content, using appropriate additives, and developing specific polymer matrix compositions.
  • compositions of the present invention for oral use include tablets containing the active ingredient(s) in a mixture with non-toxic pharmaceutically acceptable excipients.
  • excipients may be, for example, inert diluents or fillers (e.g., sucrose and sorbitol), lubricating agents, glidants, and anti-adhesives (e.g., magnesium stearate, zinc stearate, stearic acid, silicas, hydrogenated vegetable oils, or talc).
  • Compositions for oral use may also be provided as chewable tablets, or as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent, or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium.
  • compositions to be used for in vivo administration typically must be sterile. This may be accomplished by filtration through sterile filtration membranes. Where the composition is lyophilized, sterilization using this method may be conducted either prior to or following lyophilization and reconstitution.
  • the composition for parenteral administration may be stored in lyophilized form or in solution.
  • parenteral compositions generally are placed into a container having a sterile access port, for example, an intravenous solution bag or vial having a stopper pierceable by a hypodermic injection needle.
  • the pharmaceutical composition may be stored in sterile vials as a solution, suspension, gel, emulsion, solid, or a dehydrated or lyophilized powder.
  • Such formulations may be stored either in a ready-to-use form or in a form (e.g., lyophilized) requiring reconstitution prior to administration.
  • compositions herein may also contain more than one active compound as necessary for the particular indication being treated, preferably those with complementary activities that do not adversely affect each other.
  • Such molecules are suitably present in combination in amounts that are effective for the purpose intended.
  • a pharmaceutical composition comprising an anti-myostatin Adnectin of the present invention can be administered to a subject at risk for or exhibiting pathologies as described herein using standard administration techniques including oral, parenteral, pulmonary, transdermal, intramuscular, intranasal, buccal, sublingual, or suppository administration.
  • administration of the anti-myostatin Adnectins the invention is parenteral.
  • parenteral as used herein includes intravenous, intramuscular, subcutaneous, rectal, vaginal, or intraperitoneal administration. Peripheral systemic delivery by intravenous or intraperitoneal or subcutaneous injection is preferred.
  • a therapeutically effective dose refers to a dose that produces the therapeutic effects for which it is administered.
  • An effective amount of a pharmaceutical composition to be employed therapeutically will depend, for example, upon the therapeutic context and objectives.
  • One skilled in the art will appreciate that the appropriate dosage levels for treatment will thus vary depending, in part, upon the molecule delivered, the indication for which the binding agent molecule is being used, the route of administration, and the size (body weight, body surface or organ size) and condition (the age and general health) of the patient.
  • the therapeutically effective dose can be estimated initially either in cell culture assays or in animal models such as mice, rats, rabbits, dogs, pigs, or monkeys.
  • animal models such as mice, rats, rabbits, dogs, pigs, or monkeys.
  • An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
  • the exact dosage will be determined in light of factors related to the subject requiring treatment, and may be ascertained using standard techniques. Dosage and administration are adjusted to provide sufficient levels of the active compound or to maintain the desired effect. Factors that may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination(s), reaction sensitivities, and response to therapy.
  • the anti-myostatin Adnectins of the present invention are administered at about 0.01 mg/kg to about 50 mg/kg per day, preferably 0.01 mg/kg to about 30 mg/kg per day, most preferably 0.01 mg/kg to about 20 mg/kg per day.
  • the anti-myostatin Adnectins of the present invention are administered at weekly dosages of about 1 to 50 mg, more preferably about 10-50 mg. In other embodiments, the anti-myostatin Adnectins of the present invention are administered at monthly doses of 30-200 mg, preferably 50-150 mg, and more preferably 60-120 mg.
  • the frequency of dosing will depend upon the pharmacokinetic parameters of the binding agent molecule in the formulation used.
  • a composition is administered until a dosage is reached that achieves the desired effect.
  • the composition may therefore be administered as a single dose or as multiple doses (at the same or different concentrations/dosages) over time, or as a continuous infusion. Further refinement of the appropriate dosage is routinely made. Appropriate dosages may be ascertained through use of appropriate dose-response data.
  • the anti-myostatin Adnectin may be given daily (e.g., once, twice, three times, or four times daily) or less frequently (e.g., once every other day, once or twice weekly, or monthly).
  • anti-myostatin Adnectin is suitably administered to the patient at one time or over a series of treatments.
  • an anti-myostatin Adnectin or a fusion thereof, and one or more additional therapeutic agents, whether co-administered or administered sequentially, may occur as described above for therapeutic applications.
  • Suitable pharmaceutically acceptable carriers, diluents, and excipients for co-administration will be understood by the skilled artisan to depend on the identity of the particular therapeutic agent being administered.
  • the anti-myostatin Adnectins of the invention are also useful in a variety of diagnostic applications.
  • an anti-myostatin Adnectin of the invention may be used to diagnose a disorder or disease associated with increased levels of myostatin.
  • an anti-myostatin Adnectin can be used in an assay to monitor myostatin levels in a subject being treated for a myostatin-associated condition.
  • the anti-myostatin Adnectins may be used with or without modification, and are labeled by covalent or non-covalent attachment of a detectable moiety.
  • the detectable moiety can be any one which is capable of producing, either directly or indirectly, a detectable signal.
  • the detectable moiety may be a radioisotope, such as H3, C14 or 13, P32, S35, or 1131; a fluorescent or chemiluminescent compound, such as fluorescein isothiocyanate, rhodamine, or luciferin; or an enzyme, such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • a radioisotope such as H3, C14 or 13, P32, S35, or 1131
  • a fluorescent or chemiluminescent compound such as fluorescein isothiocyanate, rhodamine, or luciferin
  • an enzyme such as alkaline phosphatase, beta-galactosidase or horseradish peroxidase.
  • any method known in the art for conjugating a protein to the detectable moiety may be employed, including those methods described by Hunter, et al., Nature 144:945 (1962 ); David, et al., Biochemistry 13:1014 (1974 ); Pain, et al., J. Immunol. Meth. 40:219 (1981 ); and Nygren, J. Histochem. and Cytochem. 30:407 (1982 ).
  • In vitro methods include conjugation chemistry well known in the art, including chemistry compatible with proteins, such as chemistry for specific amino acids, such as Cys and Lys.
  • a linking group or reactive group is used.
  • linking groups are well known in the art and include disulfide groups, thioether groups, acid labile groups, photolabile groups, peptidase labile groups and esterase labile groups.
  • Preferred linking groups are disulfide groups and thioether groups depending on the application.
  • a Cys can be engineered in a location to allow for activity of the protein to exist while creating a location for conjugation.
  • Anti-myostatin Adnectins linked with a detectable moiety also are useful for in vivo imaging.
  • the polypeptide may be linked to a radio-opaque agent or radioisotope, administered to a subject, preferably into the bloodstream, and the presence and location of the labeled protein in the subject is assayed. This imaging technique is useful in the staging and treatment of malignancies.
  • the protein may be labeled with any moiety that is detectable in a subject, whether by nuclear magnetic resonance, radiology, or other detection means known in the art.
  • Anti-myostatin Adnectins also are useful as affinity purification agents.
  • the polypeptides are immobilized on a suitable support, such a Sephadex resin or filter paper, using methods well known in the art.
  • Anti-myostatin Adnectins can be employed in any known assay method, such as competitive binding assays, direct and indirect sandwich assays, and immunoprecipitation assays ( Zola, Monoclonal Antibodies: A Manual of Techniques, pp. 147-158 (CRC Press, Inc., 1987 )).
  • a method may comprise contacting the sample with an anti-myostatin Adnectins described herein, wherein said contacting is carried out under conditions that allow anti-myostatin Adnectin-target complex formation; and detecting said complex, thereby detecting said target in said sample.
  • Detection may be carried out using any art-recognized technique, such as, e.g., radiography, immunological assay, fluorescence detection, mass spectroscopy, or surface plasmon resonance.
  • the sample may be from a human or other mammal.
  • the anti-myostatin Adnectins may be labeled with a labeling moiety, such as a radioactive moiety, a fluorescent moiety, a chromogenic moiety, a chemiluminescent moiety, or a hapten moiety.
  • a labeling moiety such as a radioactive moiety, a fluorescent moiety, a chromogenic moiety, a chemiluminescent moiety, or a hapten moiety.
  • the anti-myostatin Adnectins may be immobilized on a solid support.
  • the anti-myostatin Adnectin of the invention can be provided in a kit, a packaged combination of reagents in predetermined amounts with instructions for use in the therapeutic or diagnostic methods of the invention.
  • an article of manufacture containing materials useful for the treatment or prevention of the disorders or conditions described above comprises a container and a label.
  • Suitable containers include, for example, bottles, vials, syringes, and test tubes.
  • the containers may be formed from a variety of materials such as glass or plastic.
  • the container holds a composition of the invention which is effective for preventing or treating the disorder or condition and may have a sterile access port (for example the container may be an intravenous solution bag or a vial having a stopper pierceable by a hypodermic injection needle).
  • the active agent in the composition is an anti-myostatin Adnectin of the invention.
  • the label on, or associated with, the container indicates that the composition is used for treating the condition of choice.
  • the article of manufacture may further comprise a second container comprising a pharmaceutically-acceptable buffer, such as phosphate-buffered saline, Ringer's solution and dextrose solution. It may further include other materials desirable from a commercial and user standpoint, including other buffers, diluents, filters, needles, syringes, and package inserts with instructions for use.
  • Cell pellets (in 24-well format) were lysed by resuspension in 450 ⁇ l of Lysis buffer (50 mM NaH 2 PO 4 , 0.5 M NaCl, 1x Complete TM Protease Inhibitor Cocktail-EDTA free (Roche), 1 mM PMSF, 10 mM CHAPS, 40 mM imidazole, 1 mg/ml lysozyme, 30 ⁇ g/ml DNAse, 2 ⁇ g/ml aprotonin, pH 8.0) and shaken at room temperature for 1-3 hours.
  • Lysis buffer 50 mM NaH 2 PO 4 , 0.5 M NaCl, 1x Complete TM Protease Inhibitor Cocktail-EDTA free (Roche), 1 mM PMSF, 10 mM CHAPS, 40 mM imidazole, 1 mg/ml lysozyme, 30 ⁇ g/ml DNAse, 2 ⁇ g/ml aprotonin, pH 8.0
  • Lysates were cleared and re-racked into a 96-well format by transfer into a 96-well Whatman GF/D Unifilter fitted with a 96-well, 1.2 ml catch plate and filtered by positive pressure.
  • the cleared lysates were transferred to a 96-well Nickel or Cobalt-Chelating Plate that had been equilibrated with equilibration buffer (50 mM NaH 2 PO 4 , 0.5 M NaCl, 40 mM imidazole, pH 8.0) and were incubated for 5 min. Unbound material was removed by positive pressure.
  • equilibration buffer 50 mM NaH 2 PO 4 , 0.5 M NaCl, 40 mM imidazole, pH 8.0
  • the resin was washed twice with 0.3 ml/well with Wash buffer #1 (50 mM NaH 2 PO 4 , 0.5 M NaCl, 5 mM CHAPS, 40 mM imidazole, pH 8.0). Each wash was removed by positive pressure. Prior to elution, each well was washed with 50 ⁇ l Elution buffer (PBS + 20 mM EDTA), incubated for 5 min, and this wash was discarded by positive pressure. Protein was eluted by applying an additional 100 ⁇ l of Elution buffer to each well.
  • Wash buffer #1 50 mM NaH 2 PO 4 , 0.5 M NaCl, 5 mM CHAPS, 40 mM imidazole, pH 8.0. Each wash was removed by positive pressure. Prior to elution, each well was washed with 50 ⁇ l Elution buffer (PBS + 20 mM EDTA), incubated for 5 min, and this wash was discarded by positive pressure. Protein was eluted by applying an additional 100 ⁇ l of
  • the plate(s) were centrifuged for 5 minutes at 200 g and eluted protein collected in 96-well catch plates containing 5 ⁇ l of 0.5 M MgCl 2 added to the bottom of elution catch plate prior to elution. Eluted protein was quantified using a total protein assay with wild-type 10 Fn3 domain as the protein standard.
  • Cell lysis was achieved by high pressure homogenization ( ⁇ 18,000 psi) using a Model M-110S Microfluidizer (Microfluidics).
  • the insoluble fraction was separated by centrifugation for 30 minutes at ⁇ 23,300 g at 4°C.
  • the insoluble pellet recovered from centrifugation of the lysate was washed with 20 mM sodium phosphate/500 mM NaCl, pH7.4.
  • the pellet was resolubilized in 6 M guanidine hydrochloride in 20 mM sodium phosphate/500 mM NaCl pH 7.4 with sonication, followed by incubation at 37 degrees for 1-2 hours.
  • the resolubilized pellet was filtered with a 0.45 ⁇ m filter and loaded onto a Histrap column equilibrated with the 20 mM sodium phosphate/500 mM NaCl/6 M guanidine pH7.4 buffer. After loading, the column was washed for an additional 25 column volumes with the same buffer. Bound protein was eluted with 50 mM imidazole in 20 mM sodium phosphate/500 mM NaCl/6 M guanidine-HCl, pH 7.4. The purified protein was refolded by dialysis against 50 mM sodium acetate/150 mM NaCl, pH 4.5 or PBS, pH 7.2.
  • the purification of soluble binders may also be used.
  • selected clone(s), followed by the HIS 6 tag were cloned into a pET9d vector and expressed in E.coli BL21 DE3 plysS cells. Twenty ml of an inoculum culture (generated from a single plated colony) were used to inoculate 1 liter of LB medium or TB-Overnight Expression Media (auto induction) containing 50 ⁇ g/ml Kanamycin and 34 ⁇ g/ml chloramphenicol.
  • Cultures in LB medium were incubated at 37°C until A 600 0.6-1.0, followed by induction with 1 mM isopropyl- ⁇ -thiogalactoside (IPTG) and grown for 4 hours at 30°C.
  • Cultures grown in TB-Overnight Expression Media were incubated at 37°C for 5 hours, after which the temperature was lowered to 18°C and they were grown for 19 hours. Cultures were harvested by centrifugation for 30 minutes at ⁇ 10,000 g at 4°C. Cell pellets were frozen at -80°C.
  • the thawed cell pellet was resuspended in 25 ml of lysis buffer (20 mM NaH 2 PO 4 , 0.5 M NaCl, 1x Complete TM Protease Inhibitor Cocktail-EDTA free (Roche), pH 7.4) using an Ultra-turrax homogenizer (IKA works) on ice.
  • Cell lysis was achieved by high pressure homogenization ( ⁇ 18,000 psi) using a Model M-110S Microfluidizer (Microfluidics).
  • the soluble fraction was separated by centrifugation for 30 minutes at ⁇ 23,300 g at 4°C. The supernatant was clarified using a 0.45 ⁇ m filter.
  • the clarified lysate is loaded onto a Histrap column (GE) pre-equilibrated with 20 mM sodium phosphate/500 mM NaCl, pH 7.4.
  • the column was then washed with 25 column volumes of the same buffer, followed by 20 column volumes of 20 mM sodium phosphate/500 mM NaCl/25 mM imidazole, pH 7.4 and then 35 column volumes of 20 mM sodium phosphate/500 mM NaCl/40 mM imidazole, pH 7.4.
  • Protein was eluted with 15 column volumes of 20 mM sodium phosphate/500 mM NaCl/500 mM imidazole, pH 7.4, fractions were pooled based on absorbance at A 280 , and dialyzed against 1x PBS or 50 mM Tris, 150 mM NaCl, pH 8.5 or 50 mM NaOAc, 150 mM NaCl, pH4.5. Precipitates were removed by filtering with a 0.22 ⁇ m filter.
  • Adnectins containing an engineered cysteine residue were conjugated with PEG or cysteine-blocking reagent via Michael-addition chemistry between the thiol group on the cysteine and the maleimide functional group of the PEG or n-ethylmaleimide (NEM).
  • NEM n-ethylmaleimide
  • PEGylation with 2-branched 40kDa PEG NOF Corporation, P/N GL2-400MA
  • PEG was added in molar excess to the protein solution under slightly acidic to neutral conditions. The reaction was allowed to proceed at room temperature for 2 hours to overnight. The reaction was then applied to an ion exchange column to separate the PEGylated Adnectin from the unreacted PEG-maleimide and non-PEGylated Adnectin.
  • the Adnectin was purified from SP FF in citrate buffer, pH 6.5. Following reduction with DTT, the sample was desalted on a G25 column into the same buffer to remove DTT and reacted with 20kDa bis-PEG or 4-branched 40K PEG at a 2:1 (PEG:adnectin) ratio for 2 hours at room temperature, and the reaction stopped with the addition of excess BME.
  • the sample was purified by a Resource 15S column (GE #17-0944-10) to selectively remove un-PEGylated species (and mono-PEGylated species in the case of 20kDa bis-PEG reaction).
  • a final preparative SEC column (GE #17-1071-01, Superdex200, 26/60) was used (if needed) to remove high molecular species and unreactive Adnectin.
  • NEM Pulle Chemical
  • citrate (pH 6.5) buffer was incubated for 1 hour at room temperature and the reaction stopped by the addition of excess BME.
  • the sample was then extensively dialysed against PBS.
  • the purified conjugated adnectins were analyzed by SDS-PAGE and size exclusion chromatography.
  • Selected binders were cloned into a pET9d vector with no HIS 6 tag and expressed in E.coli BL21 DE3 plysS cells.
  • 25 ml of an inoculums culture previously isolated from a single plated colony were grown in a 125 ml flask until OD 600 nm reached 1-2, using pH 6.85 media + 50ug/ml kanamycin (Ammonium Chloride, Citric Acid, Ferric Ammonium Citrate, Magnesium Sulfate, Sodium Phosphate Monobasic Monohydrate, Dextrose Anhydrous, Glycerol, Phytone Peptone, Yeast Extract Granulated, Kanamycin Sulfate, Ammonium Sulfate for pH adjustment).
  • a 10 L fermentor (7.5 L starting volume of batch media) was inoculated at a final OD 600 nm of 0.003.
  • the culture was grown overnight at 25°C with constant mixing at 650 rpm and dissolved O 2 levels of >30%, while maintaining pH.
  • the next day the temperature was shifted to 37°C and the culture was grown until OD 600 nm reached 20-25. Once the target OD was achieved, the temperature was shifted to 30°C and the culture induced with IPTG (final concentration: 1 mM).
  • a feed media (Glycerol, Phytone Peptone, Yeast Extract Granulated, Kanamycin Sulfate, and Phosphoric Acid for pH adjustment) was added at a rate of 40 ml media/L formation volume/hr. Cells were harvested by centrifugation at 10,000g for 30min at 4°C. Cell pellets were frozen at -80°C.
  • the SP1 elution was diluted 1:5 with 20 mM sodium phosphate (pH 6.7) and loaded onto a SP FF column (SP2) pre-equilibrated with 20 mM sodium phosphate/100 mM NaCl, pH 6.7. The column was then washed with 2 column volumes of the same buffer. Protein was eluted from the column with 20 mM sodium phosphate/0.5 M NaCl, pH 6.7. Elutions were pooled based on absorbance at A 280 .
  • the SP2 elution was diluted to 100 mM NaCl with 20 mM sodium phosphate (pH 6.7) and loaded onto a Q FF column (GE) pre-equilibrated with 20 mM sodium phosphate/100 mM NaCl, pH 6.7.
  • the FT peak (containing product) was collected.
  • the column was washed with equilibration buffer until the FT peak returned to baseline.
  • Adnectins containing an engineered cysteine residue were conjugated with PEG via Michael-addition chemistry between the thiol group on the cysteine and the maleimide functional group of the PEG reagent.
  • the Q FT fraction was PEGylated with 40kDa branched PEG at a molar ratio of 2:1 PEG to protein.
  • the sample was incubated overnight at room temperature.
  • the PEGylation reaction was diluted with 2 parts 50 mM sodium acetate (pH 4.5) and loaded onto a SP FF column (GE) pre-equilibrated with 50 mM sodium acetate (pH 4.5). The column was washed with 2 column volumes of the same buffer.
  • PEGylated protein was eluted from the column with 50 mM sodium acetate/200 mM NaCl, pH 4.5). Elutions were pooled based on absorbance at A 280 . PEGylated protein was concentrated using a 30kDa Millipore Biomax membrane. The sample was filtered over a 0.22 ⁇ m filter and stored at, for example, 4°C, -20°C, or -80°C.
  • pDV-16 is a modified version of pTT5 (Yves Durocher, NRC Canada), wherein the human IgG1-Fc coding sequence has been introduced, preceded by signal sequence, and restriction sites were included to allow insertion of Adnectin coding sequences at either terminus of the Fc.
  • Transformed cells were expanded by inoculating 1 L of Luria broth containing 100 ⁇ g/ml Ampicillin and incubating in a rotating incubator at 225 rpm for 18 hours at 37°C. Bacterial pellets were harvested by centrifugation at >10000g for 30 minutes at 4°C. Purified plasmid DNA was isolated using a QIAGEN Plasmid Plus Mega Kit (QIAGEN) as described in the manufacturer's protocol. Purified DNA was quantified using absorbance at 260nm and frozen at -80°C prior to use.
  • QIAGEN QIAGEN Plasmid Plus Mega Kit
  • HEK 293-EBNA1 (clone 6E) (Yves Durocher, NRC Canada) cells were expanded to 2x10 6 cells/ml in 2 L of F17 media in a 10 L GE Healthcare Wave bag at 37°C, 5% CO 2 , and mixed by rocking at an 8 degree angle at 18 rpm.
  • DNA was prepared for transfection as follows: F17 media was warmed to 37°C. DNA and a PEI transfection reagent were thawed in a sterile biosafety hood. DNA (2.25 mg) was added to 100 ml of warmed F17 media in a sterile polypropylene culture flask and gently mixed by swirling. In a separate flask, 6.75 mg of PEI (1 mg/ml) was combined with 100 ml of prewarmed F17 media and gently mixed by swirling. The flasks were allowed to rest for 5 minutes prior to combining the contents by adding the PEI solution to the flask containing the DNA and gently mixing by swirling.
  • the contents of the flask containing the DNA:PEI mixture were added to the wave bag containing the HEK 293-6E cells after incubating at room temperature for 15 minutes in the biosafety hood.
  • the bag containing the transfected HEK 293-6E cells was incubated for twenty four hours at 37°C, 5% CO 2 , and mixed by rocking at an 8 degree angle at 18 RPM. After 24 hours, 100 ml of sterile filtered 20% Tryptone N1 (Organotechnie, Canada) dissolved in F17 media was aseptically added to the culture. The cells and media were harvested after an additional 72 hours of incubation as described above.
  • transient HEK expression in shake flasks (0.5 L media in a 2 L flask) can be performed with a DNA:PEI ratio of 1:2.
  • Cells were separated from the conditioned media by centrifugation at 6000g for 30 minutes at 4°C.
  • the conditioned media was retained, filtered through a 0.2 ⁇ M filter, and stored at 4°C.
  • the conditioned media was applied to a 10 ml chromatography column containing GE MabSelect Sure resin pre-equilibrated in PBS at a rate of 5 ml/minute. After loading the filtered conditioned media, the column was washed with at least 100 ml of PBS at room temperature. The purified product was eluted from the column with the application of 100 mM Glycine/100 mM NaCl, pH 3.0. Fractions were neutralized in pH either by collecting into tubes containing 1/6 volume of 1M Tris pH 8, or by pooling according to A280 absorbance followed by addition of 1M Tris pH 8 to 100 mM.
  • the sample is further purified by a Superdex 200 (26/60) column (GE Healthcare) in PBS.
  • the SEC fractions containing monomers are pooled and concentrated.
  • the resulting protein A or SEC pool was exhaustively dialyzed against PBS at 4°C, and sterile filtered using a 0.22 ⁇ m cutoff filter prior to freezing at -80°C.
  • REB mammalian Research Cell Bank
  • UCOE Ubiquitous Chromatin Opening Element
  • An RCB was established by expanding cells in selection media (0.04% (v/v) L-Glutamine (Invitrogen) and 0.01% (v/v) HT Supplement (Invitrogen) in CD CHO medium (Invitrogen)) containing 12.5 ⁇ g/mL puromycin.
  • Cell culture was initiated by thawing a single RCB vial into 25 mL of selection media containing 12.5 ⁇ g/mL puromycin and expanding the culture in the same media. Cells were allowed to reach a concentration between 1-2 x 10 6 cells/mL before being split back to 0.2 x 10 6 cells/mL. Cells were generally maintained between 2-4 weeks prior to seeding a bioreactor.
  • the expansion culture was passaged a final time and allowed to grow to the point where a 15 L bioreactor containing 8 L of production media (Invitrogen CD CHO media containing 0.01% (v/v) HT Supplement (Invitrogen), 0.04% (v/v) Glutamax (Gibco), and 0.005% (v/v) Pluronic F-68 (Gibco)) could be seeded at a final density of 0.2 x 10 6 cells/mL.
  • the bioreactor culture was monitored daily for VCD (Viable Cell Density), percent Viability, pH, and glucose concentration.
  • the bioreactor culture was fed on days 3 and 6 with a 10% total volume bolus addition of Feed Media.
  • the culture was harvested between Day 7 and Day 9 with a percent viability >70%.
  • the bioreactor culture was controlled at a pH of 7.1, temperature of 37°C, %DO2 of 40%, and a constant RPM of 100.
  • the Protein A elution is diluted to pH 3.0 with the addition of 2 M Citric Acid and left at room temperature for 1 hour, for viral inactivation. Sample is then diluted with 200 mM Sodium Phosphate Tribasic until pH 4.5 is reached. If necessary, the solution is further diluted with water to lower conductivity below 10ms/cm.
  • the diluted Protein A elution is passed over a Tosoh Q 600C AR (Tosoh Bioscience), previously conditioned with 50mM Sodium Acetate pH 4.5, in a negative capture mode.
  • the flowthrough peak is collected, based on absorbance at A280.
  • the column is washed with 50mM Sodium Acetate and stripped with 0.2N NaOH.
  • the Q 600C AR flowthrough is formulated using tangential flow filtration utilizing a 30K NMWCO hollow fiber membrane (GE), with very gentle mixing of the retentate.
  • the adnectin-Fc fusion is diafiltered into 25mM Sodium Phosphate 150mM Trehalose pH 7.0 for 6 diavolumes, and then concentrated to a target protein concentration.
  • Size exclusion chromatography Standard size exclusion chromatography (SEC) was performed on candidate Adnectins resulting from the midscale process.
  • SEC of midscaled material was performed using a Superdex 200 10/30 or on a Superdex 75 10/30 column (GE Healthcare) on an Agilent 1100 or 1200 HPLC system with UV detection at A214 nm and A280 nm and with fluorescence detection (excitation 280 nm, emission 350 nm).
  • a buffer of 100 mM sodium sulfate/100 mM sodium phosphate/150 mM sodium chloride, pH 6.8 was used at the appropriate flow rate for the SEC column employed.
  • TSF Thermal Scanning Fluorescence
  • 3116_A07 as an unmodified Adnectin has a Tm by TSF of 60°C, but when PEGylated (ATI-1377) the Tm by DSC was 68°C, and in an Fc-X format (PRD-1286) the Tm by DSC was 66°C.
  • a luciferase reporter plasmid A ctivin- R esponsive E lement (ARE)-luc, was generated by ligating nine repeats of the ARE in tandem to the firefly luciferase reporter.
  • the plasmid was transiently transfected into HepG2 cells. Plasmid pGL4.74[hRluc/TK] was co-transfected to normalize for transfection efficiency. 10,000 cells were plated per well in a 96-well plate. When a protein such as myostatin, activin, or BMP-11, is added to cells and binds to its cognate receptor, downstream SMAD signaling is triggered, leading to binding of a phosphorylated SMAD complex to the ARE.
  • a protein such as myostatin, activin, or BMP-11
  • the amount of, e.g., myostatin, exposed to the cells is directly proportional to the amount of luciferase protein produced and, consequently, luciferase activity measured.
  • a myostatin antagonist e.g., an anti-myostatin Adnectin
  • activation of the ARE decreases, leading to a decreased luciferase production and activity.
  • anti-myostatin Adnectins inhibited myostatin-mediated increases in ARE-luc reporter activity.
  • An HTRF assay was used to measure the binding affinities of anti-myostatin Adnectins to myostatin.
  • the assay was a competitive HTRF assay using Eu-W1024 label as a donor fluorophore and Alexa Fluor® 647 as an acceptor fluorophore.
  • the biotinylated Adnectin 1889E01 and Alexa Fluor® 647 labeled rhActRIIb-Fc can bind myostatin simultaneously at two distinct binding sites.
  • the Eu-W1024 labeled Streptavidin is used to bind biotinylated 1889E01.
  • the two fluorophores, Eu-W1024 and Alexa Fluor® 647, are brought together by the formation of a 1889E01/myostatin/ActRIIb-Fc complex, and the HTRF signal can be read on an EnVision platereader (Perkin Elmer) using an HTRF protocol. In the presence of a competitive Adnectin, the HTRF signal decreases.
  • IC50s are presented in Tables 8-10. Table 8: Biophysical characterization, ARE-luciferase reporter assay, and HTRF binding assay results for anti-myostatin mono-Adnectins.
  • SMAD2 phosphorylation detected using an ELISA assay (Cell Signaling Technologies).
  • the inhibition achieved by the concentration range of Adnectins was plotted using GraphPad Prism Software and normalizing data points to controls which gave 100% and 0% inhibition.
  • the IC50 is defined as the concentration of Adnectin required to reach 50% inhibition of myostatin-induced SMAD2 phosphorylation.
  • the data presented in Table 11 indicate that Adnectins derived from affinity optimization of parental clones 1979_B06 and 2062_G02 both potently and completely inhibited myostatin-induced pSMAD phosphorylation and demonstrated IC50 values ranging from 0.78 nM to 0.06 nM.
  • Anti-human Fc antibody (Biacore/GE) was immobilized on a Biacore CM5 chip via NHS/EDC coupling according to the manufacturer's instructions. ActRIIb-Fc (R&D Systems) was captured on both reference and active flow cells, followed by capture of human myostatin (R&D Systems), human BMP-11 (GDF-11; R&D Systems), or human Activin A (R&D Systems) on active flow cells only (each solubilized according to manufacturer's suggested protocol and diluted in HBSP running buffer). A concentration range of anti-myostatin Adnectin was applied across all flow cells in HBSP running buffer. Regeneration of the chip surface between cycles was accomplished with two 30 second pulses of 3M MgCl 2 . Kinetic traces of reference-subtracted sensorgrams were fit to a 1:1 binding model using Biaevaluation software. A summary of Biacore kinetic data is shown in Table 12.
  • Adnectin selectivity over BMP-11 ranges from entirely non-selective to up to 17-fold, whereas binding to activin is either extremely weak or non-existent, suggesting high selectivity over activin.
  • Adnectin binding kinetics using SPR format B (useful for Fc-formatted adnectins)
  • the solution affinity of PRD-1474, an Fc-fused anti-myostatin Adnectin, for myostatin was measured using a Kinetic Exclusion Assay (KinExA).
  • KinExA Kinetic Exclusion Assay
  • the relative unbound myostatin concentration was measured by capture on an ATI-1310 solid matrix (coupled to polyacrylamide beads via an engineered free cysteine) followed by detection with a fluorescent-labeled construct of the myostatin co-receptor, ActRIIB-Ig which can bind myostatin simultaneously with the Adnectin.
  • ATI-1310 is a related Adnectin which competes with PRD-1474 for binding to myostatin and allows for capture of unbound myostatin.
  • the global Kd analysis shown in Table 13 gives a Kd of 170 pM with a 95% confidence interval of 330-60 pM.
  • Adnectin Kd 95% confidence interval Kd high Kd low PRD-1474 170 pM 330 pM 60 pM PRD-1177 250 pM 340 pM 130 pM ATI-1338 850 pM 1400 pM 330 pM
  • Deep Mutational Scanning High throughput sequencing was combined with protein display to allow simultaneous measurement of the relative fitness of every possible single-site loop mutant, on a scale that would be onerous for a traditional approach like that described above (for review of "Deep Mutational Scanning” approaches, see Araya et al., Trends in Biotechnology 29: 435-442, 2011 ; a similar approach is further exemplified in Forsyth et al., mAbs 5: 523-532, 2013 ).
  • the oligonucleotides were assembled via overlap extension PCR to generate the full-length Adnectin libraries, where Lib-BC contained every single amino acid BC loop mutation of 3116_A06, Lib-DE contained contained every single amino acid DE loop mutation of 3116_A06, and Lib-FG contained every single amino acid FG loop mutation of 3116_A06.
  • the three libraries were expressed as mRNA-protein fusion molecules using PROfusion according to Xu et al., Chemistry & Biology 9: 933-942, 2002 .
  • Lib-BC, Lib-DE, and Lib-FG PROfusion molecules were separately selected against 3 nM biotinylated myostatin, and binding molecules were subsequently captured on streptavidin magnetic beads.
  • the binders were eluted from the beads using 100 mM KOH.
  • the molecules eluted from the beads represent variants of 3116_A06 that can still bind to myostatin, while those present in the initial library but not found in the elution represent variants of 3116_A06 that do not bind as well to myostatin.
  • NGS ERs define a profile of enrichment and depletion of alanine mutants across the loops that correlates well with the impact observed in HTRF and ARE-luciferase assays.
  • the biochemical HTRF IC50 was also plotted directly versus the NGS ER norm for each alanine mutant, as shown in Figure 9 .
  • Table 15 Single site mutations in the loop sequences of 3116_A06 that maintain binding to myostatin Position Preferable Mutations More Preferable Mutations Most Preferable Mutations 25 X 51 ACDFHIKLNQRSTVWY CFISVWY FSW 26 X 52 LMV L L 27 X 53 ACDEIKLMNPQRSTVY P P 28 X 54 ACDEFGHIKLMNQRSTVWY CFGIKLMNRSTVWY 29 X 55 ACDEFGHIKLMNPQRSTVWY ACEFHIKLMPQRSTVY 30 X 56 GS G G G 31 X 57 ACDEFGHIKLMNQRSTVWY ACGHIKLMNQRSVWY ACHKLMNRVWY 32 X 58 ACGLMST AGLMS AGL 33 X 59 ACFHNPQRSY CHNQSY HNQ 55 G G G 56 R R R 57 G G G G 58 X 60 ACDEFIKLMNQSTV CEILMQTV
  • BC loop positions 25, 26, 27, 30, 32, and 33, DE loop positions 55, 56, and 57, and FG loop positions 80 and 88 appear to be the most conserved, where only a single or a few amino acid types at these positions maintain binding to myostatin.
  • other positions are highly tolerant to mutation, including BC loop positions 28, 29, and 31, and FG loop positions 82, 83, and 87.
  • anti-myostatin Adnectin 2987_H07 was formatted with 2-branched 40 KD PEG (ATI-1338), 4-branched 40 KD PEG (ATI-1339), and Bis 20 KD PEG (ATI-1341).
  • Single dose studies of subcutaneous administration with these three PEGylated Adnectins were conducted in C57BL6 mice. Total drug concentrations were determined by ELISA assay.
  • Bioanalytical PK immunoassay for the quantitation of ATI-1338 used a standard sandwich format ELISA assay, where the 1338 was captured with a monoclonal antibody to HIS-TAG protein, then detected with a polyclonal anti-PEG antibody.
  • the two 40 KD PEGylated formats, ATI-1338 and ATI-1339 provided more prominent pharmacokinetic enhancement (i.e., longer half life (t 1/2 ) and higher dose-normalized exposure) than the Bis-20 KD PEGylated format, ATI-1341.
  • Table 16 shows how the two 40 KD PEGylated formats, ATI-1338 and ATI-1339, provided more prominent pharmacokinetic enhancement (i.e., longer half life (t 1/2 ) and higher dose-normalized exposure) than the Bis-20 KD PEGylated format, ATI-1341. Table 16.
  • Myostatin (10 nM; R&D Systems) was preincubated with a concentration range of Adnectin or ActRIIb-Fc competitor (0.2 pM to 1 ⁇ M) in OptEIA buffer for 1 h at 25°C with shaking.
  • the blocked and coated assay plate was washed with PBS-T, and then myostatin/competitor mixtures were added and incubated for 30 min at 25°C with shaking.
  • the assay plate was washed with PBS-T, after which bound myostatin was detected with 1:1000 biotinylated goat anti-myostatin polyclonal (R&D Systems) diluted in OptEIA, for 1 h at 25°C with shaking.
  • sensor chip surfaces were prepared by immobilizing 100 ug/ml protein A (Pierce) in 10 mM acetate pH 4.5 to 4500 RU on a CM5 sensor chip (Biacore/GE Healthcare) using standard ethyl(dimethylaminopropyl) carbodiimide (EDC) / N-hydroxysuccinimide (NHS) chemistry, with ethanolamine blocking.
  • ALK4-Fc (R&D Systems), ALK5-Fc (R&D Systems), ActRIIB-Fc (produced in house), an anti-myostatin/BMP11 monoclonal antibody (mAb-A) which competes for binding to myostatin with ActRIIB but does not compete with 3116A06 for binding to mysotatin (produced in house), or Adnectin-Fc PRD-1474 at concentrations of 7-13 ⁇ g/ml were captured via the Fc tail to surface densities of 1600 - 4300 RU using 60 s injections at 10 ⁇ l/min.
  • mAb-A anti-myostatin/BMP11 monoclonal antibody
  • ATI-1523 In the assays to assess the ability of ATI-1523 to block the interaction of myostatin with ALK4-Fc or ALK5-Fc, BMP-11, which also binds to ALK4-Fc and ALK5-Fc, was used as a surrogate for myostatin, since myostatin alone does not bind significantly to ALK4-Fc and ALK5-Fc under this experimental format.
  • ATI-1523 significantly reduced the binding signal for BMP11 toward ALK4-Fc (98% reduction) and ALK5-Fc (69% reduction), suggesting that the Adnectin competes for binding to myostatin with the Type I receptors.
  • Table 18 SPR binding response for 100 nM myostatin or 100 nM BMP11 in the absence or presence of 200 nM ATI-1523 on ALK4-Fc, ALK5-Fc, ActRIIB-Fc, mAb-A, or PRD-1474 surfaces.
  • Analyte ALK4-Fc ALK5-Fc ActRIIB-Fc mAb-A PRD-1474 Myostatin 100% 100% 100% 100% Myostatin + ATI-1523 1313% 1544% -2%
  • BMP11 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% 100% BMP11 + ATI-1523 2% 31% 189% 258% -1%
  • Adnectin competition using "SPR format B” The mechanism of action for anti-myostatin Adnectins was further evaluated in "SPR Format B", where myostatin or BMP11 (10 ⁇ g/ml in 10 mM acetate pH 4.5) were directly immobilized on a CM5 sensor chip surface using EDC/NHS coupling chemistry to a density of 985 RU (myostatin) or 530 RU (BMP11).
  • the running buffer for immobilization and competition experiments was 10 mM HEPES, 150 mM NaCl, 3 mM EDTA, and 0.05% v/v Surfactant P20, pH 7.4, and surfaces were regenerated between cycles using 4 injections of 50 mM NaOH for 15 s at 30 ⁇ l/min.
  • each receptor bound specifically to immobilized BMP11, whereas only ALK5-Fc and ActRIIB-monomer, but not ALK4-Fc, bound to immobilized myostatin.
  • Pre-binding of PRD-1474 significantly reduced the binding signal for ALK4-Fc towards BMP11 (70% reduction) and also reduced the binding of ALK5-Fc towards myostatin or BMP11 (35-41% reduction), but had a minimal impact on ActRIIB-monomer binding to either myostatin or BMP11 surfaces, Table 19.
  • Adnectins represent the sequence families exemplified in the current invention, and individual clones within a well-defined sequence family maintain the same binding site, the sequences covered by the current invention act by blocking ALK4/5 recruitment to the myostatin-ActRIIb complex.
  • the pharmacokinetic data further indicate that myostatin-Adnectin complex levels accumulate with time and that these complexes bind to ActRIIb, thus acting as a dominant negative inhibitor of signaling independent of free drug.
  • This unique mechanism distinguishes the anti-myostatin Adnectins of the present invention from anti-myostatin antibodies described in the literature (e.g., US 7632499 ), and indicate that the anti-myostatin Adnectins of the invention have increased activity.
  • Example 11 Mapping of Adnectin binding site on myostatin using HDX-MS:
  • the Adnectin binding site on myostatin was further evaluated using hydrogen-deuterium exchange mass spectrometry (HDX-MS).
  • the hydrogen/deuterium exchange mass spectrometry (HDX-MS) method probes protein conformation and conformational dynamics in solution by monitoring the deuterium exchange rate and extent in the backbone amide hydrogens.
  • the level of HDX depends on the solvent accessibility of backbone amide hydrogens and the conformation of the protein.
  • the mass increase of the protein upon HDX can be precisely measured by MS.
  • this technique is paired with enzymatic digestion, structural features at the peptide level can be obtained, enabling differentiation of surface exposed peptides from those folded inside, or from those sequestered at the interface of a protein-protein complex.
  • the deuterium labeling and subsequent quenching experiments are performed, followed by online pepsin digestion, peptide separation, and MS analysis.
  • the oligomeric state of the HDX-MS samples were characterized by size-exclusion chromatography coupled to a multi-angle laser light scattering detector (SEC-MALS), where the MALS-determined mass of the myostatin/Fab-A complex ( ⁇ 120 kDa) was consistent with the expected stoichiometry of one myostatin homodimer bound to two Fab-A molecules, and the MALS-determined mass of the myostatin/Fab-A/3116_A06 complex (142 kDa) was consistent with the expected stoichiometry of one myostatin homodimer bound to two Fab-A molecules plus two 3116_A06 molecules.
  • SEC-MALS multi-angle laser light scattering detector
  • reaction was quenched by adding quenching buffer (1:1, v/v) and the quenched sample was injected into Waters HDX-MS system for analysis.
  • quenching buffer (1:1, v/v)
  • quenched sample was injected into Waters HDX-MS system for analysis.
  • the observed common peptic peptides were monitored for their deuterium uptake levels in the absence/presence of 3116_A06.
  • the two peptide regions can be ranked as region 1 > 2, with region 1 having the most significant changes in deuterium uptake.
  • Fig. 13A shows the ALK4 binding site and the ActRIIB binding site mapped onto the myostatin structure (grey). Region 1 and Region 2, which were identified by the HDX-MS experiments as described in Example 11, are indicated in black. Fig.
  • 13B shows a preferred complex from docking, with the BC, DE and FG loop of 3116_A06 (black) rendered in stick, and Regions 1 and 2 of myostatin (grey) represented in space-fill.
  • residues that were identified as loop favorable mutations show key contributions.
  • residues Ser25, Leu26, and Pro27 are important as structural constraints for maintaining the overall loop conformation.
  • Ala32 fits into a small hydrophobic cleft formed at the complex interface and the backbone of the residue forms hydrogen bonds with myostatin.
  • the most preferable substitutions at position 32 are Gly or Leu, and they are predicted to fit well in place of the alanine.
  • Asn33 is involved with hydrogen bonds to nearby tryptophan residues of myostatin.
  • the most preferable substitutions at position 33 are His and Gln, which also contain sidechains that can contribute as hydrogen bond donors.
  • Residues in the DE loop are critical: the most favorable substitutions are limited to Gly55, Arg56, and Gly 57, and only conservative substitutions are preferable for Val58.
  • Arg56 is a critical residue contributing pi cation interactions with Y86 of myostatin in Region 1 as well as additional hydrogen bonds with the backbone and side chain of other Region 1 residues. For many FG loop residues, the most preferable substitutions were conservative replacements.
  • Example 13 In vivo mouse model of musculoskeletal efficacy
  • mice Male B6.SCID mice (9-13 weeks old, Jackson Laboratories, Bar Harbor, Maine) were housed in a temperature-controlled room with a reversed 12 hour light/dark cycle. Water and standard chow food were available ad libitum. Mice were randomized and distributed between treatment groups to receive either control or test compounds of the present invention based on body weight (about 20-22 g). In order to demonstrate in vivo efficacy of the compounds of the present invention, the compounds were administered either weekly (Fc-fusion anti-myostatin adnectins) or twice a week (PEGylated anti-myostatin adnectins) by subcutaneous injection. Test compounds were administered to the animals in Phosphate-Buffered Saline (PBS).
  • PBS Phosphate-Buffered Saline
  • Controls were treated with only reconstitution buffer.
  • Body weight measurements were recorded pre-randomization, on randomization day, and two to three times a week during the treatment periods and at the end of the study.
  • Lower leg muscle mass was recorded from body carcasses at the end of the study by quantitative magnetic resonance imaging (MRI, Echo Medical Systems, Tex) analysis.
  • Test groups were compared to the control group. The results show that anti-myostatin Adnectins of the invention increased percent body weight from baseline ( Fig. 14 ) and had significant anabolic effects on skeletal muscle volume ( Fig. 15 ), compared to control mice (e.g., approximately a 7-10% increase in muscle volume compared to control.
  • Magnetic resonance imaging (MRI) Magnetic resonance imaging
  • MRI for leg muscle volume measurements were performed on a Bruker PharmaScan 4.7 Tesla with a 16 cm bore (Bruker Biospin, Billerica, Ma. USA). A 62 mm volume coil was used for the transmitter and receiver. After collection of localizer images of the lower leg, T2 weighted images were obtained using an axial slice plan.
  • the field of view was 5 cm by 2.5 cm, with a 1.25 mm slice thickness and a RARE factor of 4 and 8 signal averages.
  • Leg muscle volumes were calculated by summation of all axial slice areas multiplied by the 1.25 mm slice thickness for total muscle volume in each leg. Images were analyzed as an area average of the region-of-interests (ROI) by Image Sequence Analysis (ISA, Bruker Biospin, Billerica, Ma.). Manual ROIs were drawn around the leg muscle excluding the skin and subcutaneous fat area. The total average muscle volume for both legs is shown in Fig. 15 .
  • ROI region-of-interests
  • MRI for heart volumes as a safety end point was also performed with the same MRI scanner. After obtaining initial localizer images of the thoracic area, 9 axial images were collected from the great vessels to the apex of the heart. Similar to the analysis of leg muscles, the axial areas were added and multiplied by the slice thickness of 1.25 mm to obtain the total heart volume for each animal. No significant change in heart volume was observed by MRI.
  • PRD-1474 at 1 mg/kg showed a significant 11.1% increase in lower leg muscle volume compared to the PBS control group (p ⁇ 0.0001).
  • Significant increases in lower leg muscle volume of 27.7%, 29.7%, and 32.8% were also observed with PRD-1474 at 10 mg/kg, 30 mg/kg, and 100 mg/kg, respectively.
  • No change in heart volume was observed in all treatment dose groups relative to control. Data are presented as mean ⁇ standard deviation. The various dosage groups were compared using ANOVA. (*p ⁇ 0.0001; # not significant between groups).
  • the anti-myostatin Adnectins of the invention are effective at significantly lower dosages than myostatin inhibitors previously described (e.g., US 7632499 , J. Clin. Onclo. 30(Suppl):Abstr. 2516, 2012 ).
  • the anti-myostatin Adnectins of the invention provide increased efficacy at lower dosages combined with decreased undesired side effects, when administered alone or in combination with other myostatin inhibitors or other drugs, for treating muscle wasting and metabolic diseases described herein.

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EP20206702.1A 2012-09-13 2013-09-12 Fibronectinbasierte gerüstdomänenproteine zur bindung an myostatin Active EP3835310B1 (de)

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SI201332082T SI3835310T1 (sl) 2012-09-13 2013-09-12 Proteini skafold domene na osnovi fibronektina, ki se vežejo na miostatin
HRP20240676TT HRP20240676T1 (hr) 2012-09-13 2013-09-12 Proteini domena skele na bazi fibronektina koji vezuju miostatin
RS20240550A RS65556B1 (sr) 2012-09-13 2013-09-12 Proteini domena skele na bazi fibronektina koji vezuju miostatin
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EP3835310B1 (de) 2024-03-20
HK1212717A1 (zh) 2016-06-17
AU2013315482A1 (en) 2015-03-12
LT3564258T (lt) 2021-08-25
US9662373B2 (en) 2017-05-30
PT3835310T (pt) 2024-05-20
MY189682A (en) 2022-02-25
EP2895503B1 (de) 2019-03-27
EP4397675A3 (de) 2024-10-16
AU2018201273B2 (en) 2020-04-09
EP4397675A2 (de) 2024-07-10
TN2015000086A1 (en) 2016-06-29
US20140105896A1 (en) 2014-04-17
US10245302B2 (en) 2019-04-02

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